[med-svn] [cinema] 08/10: New upstream version 3.0.23
Andreas Tille
tille at debian.org
Sat Dec 2 15:28:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository cinema.
commit bb40f230ab98de419fc182930cdb21f0d9c5941a
Author: Andreas Tille <tille at debian.org>
Date: Sat Dec 2 16:26:53 2017 +0100
New upstream version 3.0.23
---
README | 10 +
bin/cinema | 84 +
bin/cinema.cygwin | 81 +
bin/cinema.pl | 78 +
classes/uk/ac/man/bioinf/Y.class | Bin 0 -> 197 bytes
.../analysis/consensus/ConsensusCalculator.class | Bin 0 -> 384 bytes
.../analysis/consensus/ConsensusIdentifier.class | Bin 0 -> 1136 bytes
.../analysis/consensus/ConsensusSequence.class | Bin 0 -> 424 bytes
.../consensus/DefaultConsensusSequence$1.class | Bin 0 -> 1021 bytes
.../consensus/DefaultConsensusSequence.class | Bin 0 -> 4645 bytes
.../analysis/consensus/PercentageIDConsensus.class | Bin 0 -> 1891 bytes
.../consensus/ThreadedConsensusSequence$1.class | Bin 0 -> 766 bytes
.../consensus/ThreadedConsensusSequence.class | Bin 0 -> 1638 bytes
.../analysis/misc/PercentageIDCalculator.class | Bin 0 -> 2985 bytes
.../misc/PercentageIDCalculatorManager.class | Bin 0 -> 1013 bytes
.../regexp/GappedSequenceCharacterIterator.class | Bin 0 -> 1080 bytes
.../regexp/SequenceCharacterIterator.class | Bin 0 -> 964 bytes
classes/uk/ac/man/bioinf/apps/cinema/Cinema.class | Bin 0 -> 2775 bytes
.../uk/ac/man/bioinf/apps/cinema/CinemaBoot.class | Bin 0 -> 2165 bytes
.../bioinf/apps/cinema/CinemaBootIdentifier.class | Bin 0 -> 687 bytes
.../man/bioinf/apps/cinema/CinemaGuiModule.class | Bin 0 -> 2550 bytes
.../ac/man/bioinf/apps/cinema/CinemaModule.class | Bin 0 -> 3866 bytes
.../apps/cinema/CinemaModuleFactoryInstance.class | Bin 0 -> 1299 bytes
.../man/bioinf/apps/cinema/CinemaProperties.class | Bin 0 -> 459 bytes
.../ac/man/bioinf/apps/cinema/CinemaShared.class | Bin 0 -> 357 bytes
.../apps/cinema/CinemaXMLParserFactory$1.class | Bin 0 -> 967 bytes
.../apps/cinema/CinemaXMLParserFactory.class | Bin 0 -> 862 bytes
.../cinema/color/AminoAcidColorMapMetaData.class | Bin 0 -> 3083 bytes
.../apps/cinema/color/CinemaColorFactory.class | Bin 0 -> 3329 bytes
.../apps/cinema/color/CinemaColorIdentifier.class | Bin 0 -> 818 bytes
...CinemaColorSelector$ClosureAbstractAction.class | Bin 0 -> 1863 bytes
.../apps/cinema/color/CinemaColorSelector.class | Bin 0 -> 2806 bytes
.../apps/cinema/color/ColorMapMetaData.class | Bin 0 -> 605 bytes
.../cinema/color/ColormapColorMapMetaData.class | Bin 0 -> 3233 bytes
.../cinema/color/DefaultColorMapMetaData.class | Bin 0 -> 3230 bytes
.../apps/cinema/color/GrayScaleVariance.class | Bin 0 -> 2029 bytes
.../InstancePerAlignmentColorMapMetaData.class | Bin 0 -> 1407 bytes
.../cinema/color/IntenseColorMapMetaData.class | Bin 0 -> 3186 bytes
.../apps/cinema/color/NullColorMapMetaData.class | Bin 0 -> 903 bytes
.../cinema/color/PedanticColorMapMetaData.class | Bin 0 -> 3189 bytes
.../PercentageIDVarianceColorMapMetaData.class | Bin 0 -> 1905 bytes
.../apps/cinema/color/TaylorColorMapMetaData.class | Bin 0 -> 3244 bytes
...dedPercentageIDVarianceColorMapMetaData$1.class | Bin 0 -> 1093 bytes
...eadedPercentageIDVarianceColorMapMetaData.class | Bin 0 -> 3061 bytes
.../cinema/color/VariableColorMapMetaData.class | Bin 0 -> 3193 bytes
.../cinema/color/VariationsColorMapMetaData.class | Bin 0 -> 3233 bytes
.../apps/cinema/color/WhiteColorMapMetaData.class | Bin 0 -> 1195 bytes
.../apps/cinema/color/ZenecaColorMapMetaData.class | Bin 0 -> 3223 bytes
.../apps/cinema/consensus/CinemaConsensus.class | Bin 0 -> 3632 bytes
.../CinemaConsensusCalculatorMetaData.class | Bin 0 -> 452 bytes
...emaConsensusDisplay$ClosureAbstractAction.class | Bin 0 -> 1708 bytes
.../cinema/consensus/CinemaConsensusDisplay.class | Bin 0 -> 7602 bytes
.../consensus/CinemaConsensusIdentifier.class | Bin 0 -> 757 bytes
.../PercentageIDConsensusCalculatorMetaData.class | Bin 0 -> 1870 bytes
...edPercentageIDConsensusCalculatorMetaData.class | Bin 0 -> 1780 bytes
.../cinema/core/AlignmentToListCellRenderer.class | Bin 0 -> 737 bytes
.../apps/cinema/core/AlignmentToListModel.class | Bin 0 -> 1343 bytes
.../apps/cinema/core/CinemaActionProvider.class | Bin 0 -> 202 bytes
.../bioinf/apps/cinema/core/CinemaCoreGui$1.class | Bin 0 -> 830 bytes
.../bioinf/apps/cinema/core/CinemaCoreGui$2.class | Bin 0 -> 622 bytes
.../bioinf/apps/cinema/core/CinemaCoreGui.class | Bin 0 -> 5222 bytes
.../apps/cinema/core/CinemaCoreIdentifier.class | Bin 0 -> 1106 bytes
.../bioinf/apps/cinema/core/CinemaCoreView$1.class | Bin 0 -> 977 bytes
.../bioinf/apps/cinema/core/CinemaCoreView.class | Bin 0 -> 5648 bytes
.../cinema/core/CinemaFramedActionProvider.class | Bin 0 -> 271 bytes
.../ac/man/bioinf/apps/cinema/core/CinemaGo.class | Bin 0 -> 1372 bytes
.../bioinf/apps/cinema/core/CinemaMenuSystem.class | Bin 0 -> 1568 bytes
.../cinema/core/CinemaModuleCoreIdentifier.class | Bin 0 -> 801 bytes
.../apps/cinema/core/CinemaSequenceMenu.class | Bin 0 -> 1405 bytes
.../apps/cinema/core/CinemaSystemEvents.class | Bin 0 -> 1496 bytes
.../apps/cinema/core/VersionInformation.class | Bin 0 -> 1411 bytes
.../group/CinemaAnchorManager$AnchorListener.class | Bin 0 -> 2342 bytes
.../apps/cinema/group/CinemaAnchorManager.class | Bin 0 -> 3210 bytes
...inemaGroup$CinemaGroupAlignmentIdentifier.class | Bin 0 -> 789 bytes
.../man/bioinf/apps/cinema/group/CinemaGroup.class | Bin 0 -> 1774 bytes
.../CinemaGroupFrame$GroupListCellRenderer.class | Bin 0 -> 1430 bytes
.../CinemaGroupFrame$GroupMemberCellRenderer.class | Bin 0 -> 949 bytes
...istBasicUI$InformativeSwappingListHandler.class | Bin 0 -> 1748 bytes
...GroupFrame$InformativeSwappingListBasicUI.class | Bin 0 -> 1687 bytes
.../apps/cinema/group/CinemaGroupFrame.class | Bin 0 -> 10137 bytes
.../apps/cinema/group/CinemaGroupIdentifier.class | Bin 0 -> 609 bytes
.../apps/cinema/group/CinemaGroupManager.class | Bin 0 -> 5251 bytes
.../apps/cinema/group/CinemaGroupModule$1.class | Bin 0 -> 1174 bytes
.../group/CinemaGroupModule$AddToGroup.class | Bin 0 -> 1192 bytes
...nemaGroupModule$DeleteGroupActionListener.class | Bin 0 -> 1800 bytes
.../apps/cinema/group/CinemaGroupModule.class | Bin 0 -> 8477 bytes
.../apps/cinema/io/AbstractSequenceInput$1.class | Bin 0 -> 2408 bytes
.../apps/cinema/io/AbstractSequenceInput.class | Bin 0 -> 3344 bytes
...stractSequenceInputParserExceptionHandler.class | Bin 0 -> 1004 bytes
.../apps/cinema/io/AbstractSequenceOutput$1.class | Bin 0 -> 853 bytes
.../apps/cinema/io/AbstractSequenceOutput$2.class | Bin 0 -> 855 bytes
.../apps/cinema/io/AbstractSequenceOutput.class | Bin 0 -> 3485 bytes
.../AbstractSequenceParserExceptionHandler.class | Bin 0 -> 994 bytes
.../apps/cinema/io/CinemaCommandLineParser.class | Bin 0 -> 3101 bytes
.../io/CinemaCommandLineParserIdentifier.class | Bin 0 -> 648 bytes
.../bioinf/apps/cinema/io/FileSequenceInput.class | Bin 0 -> 3268 bytes
.../FileSequenceInputParserExceptionHandler.class | Bin 0 -> 479 bytes
.../bioinf/apps/cinema/io/FileSequenceOutput.class | Bin 0 -> 3025 bytes
.../io/FileSequenceParserExceptionHandler.class | Bin 0 -> 464 bytes
.../cinema/io/SequenceInputModuleIdentifier.class | Bin 0 -> 793 bytes
.../cinema/io/SequenceOutputModuleIdentifier.class | Bin 0 -> 740 bytes
.../CinemaMotifFrame$MotifFormatFileChooser.class | Bin 0 -> 2438 bytes
.../apps/cinema/motif/CinemaMotifFrame.class | Bin 0 -> 13721 bytes
.../apps/cinema/motif/CinemaMotifIdentifier.class | Bin 0 -> 633 bytes
.../apps/cinema/motif/CinemaMotifModule$1.class | Bin 0 -> 1393 bytes
.../apps/cinema/motif/CinemaMotifModule.class | Bin 0 -> 2249 bytes
.../motif/NamedAlignmentSelectionModel$1.class | Bin 0 -> 1020 bytes
.../motif/NamedAlignmentSelectionModel$2.class | Bin 0 -> 1216 bytes
...amedAlignmentSelectionModel$SelectionInfo.class | Bin 0 -> 786 bytes
.../motif/NamedAlignmentSelectionModel.class | Bin 0 -> 7808 bytes
.../apps/cinema/resources/CinemaResources.class | Bin 0 -> 2940 bytes
.../bioinf/apps/cinema/shared/CinemaDebug$1.class | Bin 0 -> 887 bytes
.../bioinf/apps/cinema/shared/CinemaDebug$2.class | Bin 0 -> 887 bytes
.../apps/cinema/shared/CinemaDebug$DebugImpl.class | Bin 0 -> 955 bytes
.../bioinf/apps/cinema/shared/CinemaDebug.class | Bin 0 -> 6760 bytes
.../cinema/shared/CinemaSharedIdentifier.class | Bin 0 -> 912 bytes
.../cinema/shared/CinemaSharedQuitExit$1.class | Bin 0 -> 1630 bytes
.../cinema/shared/CinemaSharedQuitExit$2.class | Bin 0 -> 1051 bytes
.../CinemaSharedQuitExit$QuitExitManager.class | Bin 0 -> 1722 bytes
.../apps/cinema/shared/CinemaSharedQuitExit.class | Bin 0 -> 1672 bytes
.../bioinf/apps/cinema/shared/CinemaSplash.class | Bin 0 -> 1753 bytes
.../apps/cinema/utils/CinemaAlignmentFrame.class | Bin 0 -> 6034 bytes
.../bioinf/apps/cinema/utils/CinemaDebug$1.class | Bin 0 -> 882 bytes
.../bioinf/apps/cinema/utils/CinemaDebug$2.class | Bin 0 -> 882 bytes
.../apps/cinema/utils/CinemaDebug$DebugImpl.class | Bin 0 -> 949 bytes
.../man/bioinf/apps/cinema/utils/CinemaDebug.class | Bin 0 -> 6750 bytes
.../CinemaFileOptionableExceptionHandler.class | Bin 0 -> 2153 bytes
.../apps/cinema/utils/CinemaFilePersist.class | Bin 0 -> 1713 bytes
.../bioinf/apps/cinema/utils/CinemaInvoker.class | Bin 0 -> 1594 bytes
.../apps/cinema/utils/CinemaMenuBuilder.class | Bin 0 -> 2137 bytes
.../utils/CinemaMultipleConsensusViewer.class | Bin 0 -> 5516 bytes
.../bioinf/apps/cinema/utils/CinemaPersist.class | Bin 0 -> 644 bytes
.../bioinf/apps/cinema/utils/CinemaRegexp$1.class | Bin 0 -> 1342 bytes
.../utils/CinemaRegexp$FramedAbstractAction.class | Bin 0 -> 850 bytes
.../bioinf/apps/cinema/utils/CinemaRegexp.class | Bin 0 -> 3539 bytes
...CinemaResizeElements$FramedAbstractAction.class | Bin 0 -> 1411 bytes
.../utils/CinemaResizeElements$ResizerGui.class | Bin 0 -> 5633 bytes
.../apps/cinema/utils/CinemaResizeElements.class | Bin 0 -> 1619 bytes
.../cinema/utils/CinemaSlaveViewerModule.class | Bin 0 -> 2224 bytes
.../cinema/utils/CinemaStatusInformation$1.class | Bin 0 -> 1045 bytes
.../cinema/utils/CinemaStatusInformation$2.class | Bin 0 -> 699 bytes
.../cinema/utils/CinemaStatusInformation.class | Bin 0 -> 4732 bytes
.../cinema/utils/CinemaUtilityIdentifier.class | Bin 0 -> 2015 bytes
.../utils/ConsensusPercentageIDColorMap.class | Bin 0 -> 4128 bytes
.../apps/commandline/CalculatePercentageID$1.class | Bin 0 -> 513 bytes
.../apps/commandline/CalculatePercentageID.class | Bin 0 -> 1532 bytes
.../CheckMotifLocationAgainstPrints$1.class | Bin 0 -> 456 bytes
.../CheckMotifLocationAgainstPrints.class | Bin 0 -> 7869 bytes
.../apps/commandline/GappedSequenceSearch$1.class | Bin 0 -> 434 bytes
.../apps/commandline/GappedSequenceSearch.class | Bin 0 -> 2494 bytes
.../bioinf/apps/commandline/SequenceSearch$1.class | Bin 0 -> 422 bytes
.../bioinf/apps/commandline/SequenceSearch.class | Bin 0 -> 2512 bytes
.../ac/man/bioinf/apps/invoker/AnonInvoker.class | Bin 0 -> 647 bytes
.../uk/ac/man/bioinf/apps/invoker/Invoker.class | Bin 0 -> 1213 bytes
.../InvokerInternalEventQueueException.class | Bin 0 -> 545 bytes
.../apps/invoker/InvokerInternalQueue$1.class | Bin 0 -> 530 bytes
.../bioinf/apps/invoker/InvokerInternalQueue.class | Bin 0 -> 4613 bytes
.../invoker/InvokerInternalQueueException.class | Bin 0 -> 295 bytes
.../bioinf/apps/invoker/InvokerThreadManager.class | Bin 0 -> 1107 bytes
.../apps/optionable/FileSaveableOptions.class | Bin 0 -> 1151 bytes
.../bioinf/apps/optionable/NullOptionHandler.class | Bin 0 -> 778 bytes
.../man/bioinf/apps/optionable/OptionHandler.class | Bin 0 -> 272 bytes
.../ac/man/bioinf/apps/optionable/Optionable.class | Bin 0 -> 436 bytes
.../optionable/OptionableExceptionHandler.class | Bin 0 -> 426 bytes
.../OptionableSourceNotFoundException.class | Bin 0 -> 362 bytes
.../apps/optionable/OptionableStateException.class | Bin 0 -> 281 bytes
.../bioinf/apps/optionable/SaveableOptions.class | Bin 0 -> 4507 bytes
.../man/bioinf/apps/systemevents/SystemEvent.class | Bin 0 -> 544 bytes
.../apps/systemevents/SystemEventOption.class | Bin 0 -> 593 bytes
.../apps/systemevents/SystemEventProducer.class | Bin 0 -> 280 bytes
.../SystemEventSupport$ListenerToComparable.class | Bin 0 -> 1296 bytes
.../apps/systemevents/SystemEventSupport.class | Bin 0 -> 1984 bytes
.../bioinf/apps/systemevents/SystemListener.class | Bin 0 -> 520 bytes
.../apps/systemevents/SystemVetoException.class | Bin 0 -> 544 bytes
classes/uk/ac/man/bioinf/apps/xml/ConfigNode.class | Bin 0 -> 1525 bytes
.../man/bioinf/apps/xml/DefaultXMLParser$1.class | Bin 0 -> 1054 bytes
.../ac/man/bioinf/apps/xml/DefaultXMLParser.class | Bin 0 -> 829 bytes
.../ac/man/bioinf/apps/xml/XMLBootIdentifier.class | Bin 0 -> 566 bytes
.../bioinf/apps/xml/XMLBootModule$MiniStack.class | Bin 0 -> 896 bytes
.../uk/ac/man/bioinf/apps/xml/XMLBootModule.class | Bin 0 -> 8306 bytes
.../bioinf/apps/xml/XMLBootParserListener.class | Bin 0 -> 3575 bytes
classes/uk/ac/man/bioinf/apps/xml/XMLModule.class | Bin 0 -> 1015 bytes
.../ac/man/bioinf/apps/xml/XMLParserFactory.class | Bin 0 -> 190 bytes
.../database/fetch/ExpasySequenceRetriever.class | Bin 0 -> 1834 bytes
.../fetch/FetchSequenceBySwissProtID.class | Bin 0 -> 262 bytes
.../bioinf/database/fetch/SequenceRetriever.class | Bin 0 -> 472 bytes
classes/uk/ac/man/bioinf/debug/AbstractDebug.class | Bin 0 -> 1409 bytes
classes/uk/ac/man/bioinf/debug/Debug.class | Bin 0 -> 3393 bytes
.../uk/ac/man/bioinf/debug/DebugInterface.class | Bin 0 -> 746 bytes
.../uk/ac/man/bioinf/debug/DebugMultiplexer.class | Bin 0 -> 4062 bytes
classes/uk/ac/man/bioinf/debug/DefaultDebug.class | Bin 0 -> 969 bytes
.../uk/ac/man/bioinf/debug/DefaultFileDebug.class | Bin 0 -> 1234 bytes
classes/uk/ac/man/bioinf/debug/NullDebug.class | Bin 0 -> 420 bytes
.../ac/man/bioinf/gui/color/ColorGenerator.class | Bin 0 -> 802 bytes
classes/uk/ac/man/bioinf/gui/color/ColorList.class | Bin 0 -> 1340 bytes
classes/uk/ac/man/bioinf/gui/color/ColorMap.class | Bin 0 -> 352 bytes
.../man/bioinf/gui/color/ColorMapException.class | Bin 0 -> 268 bytes
.../uk/ac/man/bioinf/gui/color/ColorStore.class | Bin 0 -> 1267 bytes
.../man/bioinf/gui/color/DoubleArrayColorMap.class | Bin 0 -> 1821 bytes
.../gui/color/IndividualElementColorMap.class | Bin 0 -> 1208 bytes
.../gui/color/PercentIDVarianceColorMap.class | Bin 0 -> 2170 bytes
.../ac/man/bioinf/gui/color/SingleColorMap.class | Bin 0 -> 825 bytes
.../man/bioinf/gui/color/ThreadableColorMap.class | Bin 0 -> 213 bytes
.../man/bioinf/gui/color/ThreadedColorMap$1.class | Bin 0 -> 1041 bytes
.../ac/man/bioinf/gui/color/ThreadedColorMap.class | Bin 0 -> 3648 bytes
.../ac/man/bioinf/gui/misc/ChunkyListModel.class | Bin 0 -> 4161 bytes
...pingListBasicUI$SwappingMouseInputHandler.class | Bin 0 -> 1702 bytes
.../man/bioinf/gui/misc/SwappingListBasicUI.class | Bin 0 -> 766 bytes
.../bioinf/gui/optionable/OptionableJFrame.class | Bin 0 -> 3331 bytes
.../gui/optionable/OptionableJSplitPane.class | Bin 0 -> 2297 bytes
.../man/bioinf/gui/util/ApplicationFrame$1.class | Bin 0 -> 1545 bytes
.../ac/man/bioinf/gui/util/ApplicationFrame.class | Bin 0 -> 8393 bytes
.../ac/man/bioinf/gui/util/PopUpHtmlDisplay.class | Bin 0 -> 1541 bytes
.../uk/ac/man/bioinf/gui/util/TripletPanel.class | Bin 0 -> 2654 bytes
.../man/bioinf/gui/util/forms/DecimalField.class | Bin 0 -> 1623 bytes
.../bioinf/gui/util/forms/FormattedDocument.class | Bin 0 -> 1695 bytes
.../util/forms/IntegerField$IntegerDocument.class | Bin 0 -> 1463 bytes
.../man/bioinf/gui/util/forms/IntegerField.class | Bin 0 -> 1764 bytes
.../man/bioinf/gui/util/forms/PasswordDialog.class | Bin 0 -> 3257 bytes
.../util/forms/ValidatedForm$ModifierCombo.class | Bin 0 -> 813 bytes
.../forms/ValidatedForm$MyDocumentListener.class | Bin 0 -> 833 bytes
.../man/bioinf/gui/util/forms/ValidatedForm.class | Bin 0 -> 7373 bytes
.../WholeNumberField$WholeNumberDocument.class | Bin 0 -> 1475 bytes
.../bioinf/gui/util/forms/WholeNumberField.class | Bin 0 -> 1605 bytes
.../gui/viewer/AlignmentSelectionModel.class | Bin 0 -> 1147 bytes
.../gui/viewer/AlignmentSelectionRenderer.class | Bin 0 -> 330 bytes
.../gui/viewer/AlignmentViewerCellRenderer.class | Bin 0 -> 393 bytes
.../BorderFastAlignmentViewerCellRenderer.class | Bin 0 -> 1086 bytes
.../bioinf/gui/viewer/ButtonViewerPopupMenu.class | Bin 0 -> 1677 bytes
.../ColorFastAlignmentViewerCellRenderer.class | Bin 0 -> 835 bytes
...CursorLessFastAlignmentViewerCellRenderer.class | Bin 0 -> 678 bytes
.../viewer/DefaultAlignmentSelectionRenderer.class | Bin 0 -> 753 bytes
.../DefaultAlignmentViewerCellRenderer.class | Bin 0 -> 1633 bytes
.../DefaultFastAlignmentViewerCellRenderer.class | Bin 0 -> 1613 bytes
.../bioinf/gui/viewer/DefaultSequenceCursor.class | Bin 0 -> 1525 bytes
.../viewer/FastAlignmentViewerCellRenderer.class | Bin 0 -> 391 bytes
classes/uk/ac/man/bioinf/gui/viewer/Install.class | Bin 0 -> 1916 bytes
.../gui/viewer/InvertedScrollPaneLayout.class | Bin 0 -> 3633 bytes
...ignmentButtonPanel$SequenceButtonListener.class | Bin 0 -> 1107 bytes
.../bioinf/gui/viewer/JAlignmentButtonPanel.class | Bin 0 -> 5226 bytes
...er$SequenceAlignmentBoundRangeModelBridge.class | Bin 0 -> 2086 bytes
.../ac/man/bioinf/gui/viewer/JAlignmentRuler.class | Bin 0 -> 3546 bytes
.../man/bioinf/gui/viewer/JAlignmentViewer.class | Bin 0 -> 14791 bytes
.../man/bioinf/gui/viewer/JChangedScrollPane.class | Bin 0 -> 1142 bytes
.../man/bioinf/gui/viewer/JLayableScrollPane.class | Bin 0 -> 1142 bytes
...ultiplexerFastAlignmentViewerCellRenderer.class | Bin 0 -> 2625 bytes
.../gui/viewer/NullAlignmentSelectionModel.class | Bin 0 -> 2165 bytes
.../gui/viewer/PrintableAlignmentPanel.class | Bin 0 -> 250 bytes
.../gui/viewer/PrintableJAlignmentViewer.class | Bin 0 -> 1169 bytes
.../man/bioinf/gui/viewer/ReadonlyException.class | Bin 0 -> 865 bytes
.../ac/man/bioinf/gui/viewer/SequenceCursor.class | Bin 0 -> 437 bytes
.../gui/viewer/SingleAlignmentSelectionModel.class | Bin 0 -> 3152 bytes
.../TextFastAlignmentViewerCellRenderer.class | Bin 0 -> 1332 bytes
.../gui/viewer/event/AlignmentSelectionEvent.class | Bin 0 -> 1283 bytes
.../viewer/event/AlignmentSelectionListener.class | Bin 0 -> 286 bytes
.../event/AlignmentSelectionListenerSupport.class | Bin 0 -> 1126 bytes
.../gui/viewer/event/ChangeListenerSupport.class | Bin 0 -> 982 bytes
.../bioinf/gui/viewer/plaf/AlignmentRulerUI.class | Bin 0 -> 251 bytes
.../bioinf/gui/viewer/plaf/AlignmentViewerUI.class | Bin 0 -> 935 bytes
.../gui/viewer/plaf/BasicAlignmentRulerUI.class | Bin 0 -> 2336 bytes
.../gui/viewer/plaf/BasicAlignmentViewerUI$1.class | Bin 0 -> 928 bytes
.../gui/viewer/plaf/BasicAlignmentViewerUI$2.class | Bin 0 -> 1237 bytes
.../gui/viewer/plaf/BasicAlignmentViewerUI$3.class | Bin 0 -> 1237 bytes
.../BasicAlignmentViewerUI$CursorBlinkThread.class | Bin 0 -> 1042 bytes
.../plaf/BasicAlignmentViewerUI$KeyScroller.class | Bin 0 -> 1249 bytes
.../BasicAlignmentViewerUI$PointListener.class | Bin 0 -> 1407 bytes
.../BasicAlignmentViewerUI$SelectionClearer.class | Bin 0 -> 1002 bytes
.../BasicAlignmentViewerUI$SelectionToggler.class | Bin 0 -> 1271 bytes
.../gui/viewer/plaf/BasicAlignmentViewerUI.class | Bin 0 -> 16192 bytes
.../gui/viewer/plaf/MetalAlignmentViewerUI.class | Bin 0 -> 290 bytes
.../gui/viewer/test/BasicWindowMonitor.class | Bin 0 -> 571 bytes
.../viewer/test/CellRendererPaneReplacement.class | Bin 0 -> 1186 bytes
.../man/bioinf/gui/viewer/test/SliderExample.class | Bin 0 -> 1680 bytes
.../uk/ac/man/bioinf/io/AlignmentInputParser.class | Bin 0 -> 560 bytes
.../ac/man/bioinf/io/AlignmentOutputParser.class | Bin 0 -> 343 bytes
.../bioinf/io/DefaultParserExceptionHandler.class | Bin 0 -> 651 bytes
.../io/InvalidSequenceTypeParserException.class | Bin 0 -> 1176 bytes
.../io/NarrowedInputStream$NoisyStream.class | Bin 0 -> 1167 bytes
.../uk/ac/man/bioinf/io/NarrowedInputStream.class | Bin 0 -> 1893 bytes
.../man/bioinf/io/NullParserExceptionHandler.class | Bin 0 -> 900 bytes
classes/uk/ac/man/bioinf/io/ParserException.class | Bin 0 -> 1159 bytes
.../ac/man/bioinf/io/ParserExceptionHandler.class | Bin 0 -> 214 bytes
.../uk/ac/man/bioinf/io/SequenceInputParser.class | Bin 0 -> 352 bytes
.../ac/man/bioinf/io/SequenceWriterException.class | Bin 0 -> 361 bytes
.../ac/man/bioinf/io/UnknownElementException.class | Bin 0 -> 690 bytes
.../AbstractProteinAlignmentInputParser.class | Bin 0 -> 2453 bytes
.../AbstractProteinSequenceInputParser.class | Bin 0 -> 2495 bytes
.../bioinf/io/parsers/FastaSequenceParser.class | Bin 0 -> 1901 bytes
.../man/bioinf/io/parsers/MotProteinParser.class | Bin 0 -> 2420 bytes
.../io/parsers/PIRProteinAlignmentParser.class | Bin 0 -> 5001 bytes
.../AbstractEnumeratedModuleIdentifier.class | Bin 0 -> 1979 bytes
.../man/bioinf/module/DefaultModuleContext.class | Bin 0 -> 779 bytes
.../module/DefaultModuleFactoryInstance.class | Bin 0 -> 5646 bytes
.../bioinf/module/GenericModuleIdentifier.class | Bin 0 -> 664 bytes
classes/uk/ac/man/bioinf/module/Module.class | Bin 0 -> 3276 bytes
.../uk/ac/man/bioinf/module/ModuleContext.class | Bin 0 -> 1610 bytes
.../uk/ac/man/bioinf/module/ModuleException.class | Bin 0 -> 1169 bytes
.../ac/man/bioinf/module/ModuleExceptionType.class | Bin 0 -> 863 bytes
.../man/bioinf/module/ModuleFactoryInstance.class | Bin 0 -> 1093 bytes
.../uk/ac/man/bioinf/module/ModuleIdentifier.class | Bin 0 -> 235 bytes
.../man/bioinf/module/ModuleIdentifierList.class | Bin 0 -> 1474 bytes
classes/uk/ac/man/bioinf/module/ModuleList.class | Bin 0 -> 1337 bytes
.../man/bioinf/module/ModuleStorageStructure.class | Bin 0 -> 2931 bytes
.../man/bioinf/module/NoSuchRequiredModule.class | Bin 0 -> 574 bytes
.../ac/man/bioinf/module/NullModuleFactory.class | Bin 0 -> 1577 bytes
.../bioinf/sequence/AbstractEditableSequence.class | Bin 0 -> 2310 bytes
.../bioinf/sequence/AbstractMutableSequence.class | Bin 0 -> 1460 bytes
.../ac/man/bioinf/sequence/AbstractSequence.class | Bin 0 -> 2783 bytes
.../sequence/ComplexEditableGappedSequence.class | Bin 0 -> 421 bytes
.../bioinf/sequence/DefaultEditableSequence.class | Bin 0 -> 2564 bytes
.../ac/man/bioinf/sequence/DefaultSequence.class | Bin 0 -> 1891 bytes
.../ac/man/bioinf/sequence/EditableSequence.class | Bin 0 -> 816 bytes
classes/uk/ac/man/bioinf/sequence/Element.class | Bin 0 -> 144 bytes
.../uk/ac/man/bioinf/sequence/EmptySequence.class | Bin 0 -> 1814 bytes
.../sequence/InvalidSequenceTypeException.class | Bin 0 -> 289 bytes
.../ac/man/bioinf/sequence/MutableSequence.class | Bin 0 -> 240 bytes
.../sequence/NoSuchSequenceElementException.class | Bin 0 -> 955 bytes
classes/uk/ac/man/bioinf/sequence/Residue.class | Bin 0 -> 162 bytes
classes/uk/ac/man/bioinf/sequence/Sequence.class | Bin 0 -> 554 bytes
.../ac/man/bioinf/sequence/SequenceException.class | Bin 0 -> 267 bytes
.../ac/man/bioinf/sequence/SequenceFactory.class | Bin 0 -> 2761 bytes
.../uk/ac/man/bioinf/sequence/SequenceType.class | Bin 0 -> 534 bytes
classes/uk/ac/man/bioinf/sequence/Sequences.class | Bin 0 -> 6042 bytes
.../alignment/AbstractGappedSequence.class | Bin 0 -> 3108 bytes
.../alignment/AbstractSequenceAlignment.class | Bin 0 -> 5697 bytes
.../sequence/alignment/AlignmentColumn.class | Bin 0 -> 1692 bytes
.../sequence/alignment/DefaultGappedSequence.class | Bin 0 -> 5479 bytes
.../alignment/DefaultSequenceAlignment.class | Bin 0 -> 6369 bytes
.../sequence/alignment/EmptyGappedSequence.class | Bin 0 -> 3398 bytes
.../alignment/EmptySequenceAlignment.class | Bin 0 -> 3662 bytes
.../uk/ac/man/bioinf/sequence/alignment/Gap.class | Bin 0 -> 576 bytes
.../bioinf/sequence/alignment/GappedSequence.class | Bin 0 -> 949 bytes
.../alignment/NoGapAtThisPositionException.class | Bin 0 -> 1168 bytes
.../alignment/NoSuchSequenceException.class | Bin 0 -> 991 bytes
.../sequence/alignment/SequenceAlignment.class | Bin 0 -> 1262 bytes
.../alignment/SingleSequenceAlignment.class | Bin 0 -> 872 bytes
.../sequence/alignment/event/AlignmentEvent.class | Bin 0 -> 926 bytes
.../alignment/event/AlignmentEventProvider.class | Bin 0 -> 455 bytes
.../alignment/event/AlignmentEventType.class | Bin 0 -> 1008 bytes
.../alignment/event/AlignmentListener.class | Bin 0 -> 277 bytes
.../alignment/event/AlignmentListenerSupport.class | Bin 0 -> 1886 bytes
.../alignment/event/AlignmentVetoException.class | Bin 0 -> 581 bytes
.../alignment/event/VetoableAlignmentEvent.class | Bin 0 -> 538 bytes
.../event/VetoableAlignmentListener.class | Bin 0 -> 438 bytes
.../sequence/complex/AbstractComplexSequence.class | Bin 0 -> 4117 bytes
.../complex/AbstractComplexSequenceType.class | Bin 0 -> 1851 bytes
.../sequence/complex/AbstractModification.class | Bin 0 -> 551 bytes
.../bioinf/sequence/complex/ComplexElement.class | Bin 0 -> 401 bytes
.../sequence/complex/ComplexElementFactory.class | Bin 0 -> 1906 bytes
.../complex/ComplexElementFactoryInterface.class | Bin 0 -> 651 bytes
.../bioinf/sequence/complex/ComplexSequence.class | Bin 0 -> 750 bytes
.../sequence/complex/ComplexSequenceType.class | Bin 0 -> 507 bytes
.../sequence/complex/DefaultComplexElement.class | Bin 0 -> 2303 bytes
.../sequence/complex/DefaultComplexSequence.class | Bin 0 -> 2801 bytes
.../complex/DefaultComplexSequenceType.class | Bin 0 -> 2348 bytes
.../complex/DefaultGappedComplexSequence$1.class | Bin 0 -> 850 bytes
...lexSequence$DisabledDefaultGappedSequence.class | Bin 0 -> 1081 bytes
.../complex/DefaultGappedComplexSequence.class | Bin 0 -> 5306 bytes
.../sequence/complex/GappedComplexSequence.class | Bin 0 -> 272 bytes
.../sequence/complex/GenericModification.class | Bin 0 -> 566 bytes
.../complex/HardComplexElementFactory.class | Bin 0 -> 1844 bytes
.../complex/HardModificationSetFactory.class | Bin 0 -> 1956 bytes
.../IllegalDuplicateModificationException.class | Bin 0 -> 315 bytes
.../man/bioinf/sequence/complex/Methylation.class | Bin 0 -> 468 bytes
.../man/bioinf/sequence/complex/Modification.class | Bin 0 -> 203 bytes
.../sequence/complex/ModificationFactory.class | Bin 0 -> 2254 bytes
.../sequence/complex/ModificationSet$1.class | Bin 0 -> 577 bytes
.../bioinf/sequence/complex/ModificationSet.class | Bin 0 -> 1695 bytes
.../sequence/complex/ModificationSetFactory.class | Bin 0 -> 1220 bytes
.../complex/ModificationSetFactoryInterface.class | Bin 0 -> 648 bytes
.../complex/NoSuchModificationException.class | Bin 0 -> 295 bytes
.../sequence/complex/SingletonModification.class | Bin 0 -> 502 bytes
.../complex/WeakComplexElementFactory.class | Bin 0 -> 2653 bytes
.../complex/WeakModificationSetFactory.class | Bin 0 -> 2072 bytes
.../man/bioinf/sequence/event/SequenceEvent.class | Bin 0 -> 1289 bytes
.../sequence/event/SequenceEventProvider.class | Bin 0 -> 417 bytes
.../bioinf/sequence/event/SequenceEventType.class | Bin 0 -> 761 bytes
.../bioinf/sequence/event/SequenceListener.class | Bin 0 -> 254 bytes
.../sequence/event/SequenceListenerSupport.class | Bin 0 -> 2080 bytes
.../sequence/event/SequenceVetoException.class | Bin 0 -> 536 bytes
.../sequence/event/VetoableSequenceEvent.class | Bin 0 -> 493 bytes
.../sequence/event/VetoableSequenceListener.class | Bin 0 -> 393 bytes
.../sequence/geom/SequenceAlignmentDimension.class | Bin 0 -> 1105 bytes
.../sequence/geom/SequenceAlignmentPoint.class | Bin 0 -> 2107 bytes
.../sequence/geom/SequenceAlignmentRectangle.class | Bin 0 -> 3820 bytes
.../sequence/geom/SequenceAlignmentShape.class | Bin 0 -> 240 bytes
.../group/AbstractGappedSequenceGroup.class | Bin 0 -> 686 bytes
.../group/DefaultGappedSequenceGroup.class | Bin 0 -> 1904 bytes
.../sequence/group/GappedSequenceGroup.class | Bin 0 -> 291 bytes
.../sequence/group/GroupSequenceAlignment$1.class | Bin 0 -> 1757 bytes
.../sequence/group/GroupSequenceAlignment.class | Bin 0 -> 7941 bytes
.../man/bioinf/sequence/group/SequenceGroup.class | Bin 0 -> 488 bytes
.../sequence/identifier/AbstractIdentifier.class | Bin 0 -> 606 bytes
.../sequence/identifier/DatabaseIdentifier.class | Bin 0 -> 649 bytes
.../bioinf/sequence/identifier/FileSource.class | Bin 0 -> 547 bytes
.../bioinf/sequence/identifier/Identifiable.class | Bin 0 -> 220 bytes
.../bioinf/sequence/identifier/Identifier.class | Bin 0 -> 321 bytes
.../identifier/MalformedAccessionException.class | Bin 0 -> 306 bytes
.../bioinf/sequence/identifier/NoIdentifier.class | Bin 0 -> 960 bytes
.../man/bioinf/sequence/identifier/NoSource.class | Bin 0 -> 430 bytes
.../bioinf/sequence/identifier/ReaderSource.class | Bin 0 -> 382 bytes
.../sequence/identifier/SequenceSource.class | Bin 0 -> 188 bytes
.../sequence/identifier/SimpleIdentifier.class | Bin 0 -> 690 bytes
.../bioinf/sequence/identifier/SimpleSource.class | Bin 0 -> 447 bytes
.../ac/man/bioinf/sequence/identifier/Source.class | Bin 0 -> 172 bytes
.../sequence/identifier/StreamSequenceSource.class | Bin 0 -> 620 bytes
.../sequence/identifier/SwissProtIdentifier.class | Bin 0 -> 751 bytes
.../sequence/identifier/URLSequenceSource.class | Bin 0 -> 924 bytes
.../bioinf/sequence/types/AbstractElement.class | Bin 0 -> 774 bytes
.../types/AbstractEnumeratedSequenceType.class | Bin 0 -> 1268 bytes
.../sequence/types/AbstractSequenceType.class | Bin 0 -> 1942 bytes
.../ac/man/bioinf/sequence/types/AminoAcid.class | Bin 0 -> 3840 bytes
.../man/bioinf/sequence/types/DNANucleotide.class | Bin 0 -> 1794 bytes
.../ac/man/bioinf/sequence/types/DNAResidue.class | Bin 0 -> 190 bytes
.../bioinf/sequence/types/DNASequenceType.class | Bin 0 -> 1285 bytes
.../bioinf/sequence/types/EmptySequenceType.class | Bin 0 -> 1438 bytes
.../bioinf/sequence/types/NucleotideResidue.class | Bin 0 -> 188 bytes
.../man/bioinf/sequence/types/ProteinResidue.class | Bin 0 -> 182 bytes
.../sequence/types/ProteinSequenceType.class | Bin 0 -> 1297 bytes
.../man/bioinf/sequence/types/RNANucleotide.class | Bin 0 -> 1788 bytes
.../ac/man/bioinf/sequence/types/RNAResidue.class | Bin 0 -> 190 bytes
.../bioinf/sequence/types/RNASequenceType.class | Bin 0 -> 1285 bytes
.../util/AbstractEnumeration$ElementIterator.class | Bin 0 -> 1535 bytes
.../ac/man/bioinf/util/AbstractEnumeration.class | Bin 0 -> 2213 bytes
.../uk/ac/man/bioinf/util/ArrayManipulation.class | Bin 0 -> 1188 bytes
classes/uk/ac/man/bioinf/util/Changeable.class | Bin 0 -> 230 bytes
.../uk/ac/man/bioinf/util/ChangeableEvent.class | Bin 0 -> 254 bytes
.../uk/ac/man/bioinf/util/ChangeableListener.class | Bin 0 -> 209 bytes
.../bioinf/util/ChangeableListenerSupport.class | Bin 0 -> 1075 bytes
.../uk/ac/man/bioinf/util/CollectionPrinter.class | Bin 0 -> 1238 bytes
classes/uk/ac/man/bioinf/util/Direction.class | Bin 0 -> 611 bytes
.../uk/ac/man/bioinf/util/ExceptionHandler.class | Bin 0 -> 188 bytes
classes/uk/ac/man/bioinf/util/IntArrayList.class | Bin 0 -> 3138 bytes
.../man/bioinf/util/PackageResourceAdapter.class | Bin 0 -> 1195 bytes
.../uk/ac/man/bioinf/util/ResourceAdapter.class | Bin 0 -> 2024 bytes
.../SequenceAlignmentToChangeableAdaptor.class | Bin 0 -> 1496 bytes
classes/uk/ac/man/bioinf/util/SwingWorker$1.class | Bin 0 -> 521 bytes
classes/uk/ac/man/bioinf/util/SwingWorker$2.class | Bin 0 -> 1064 bytes
.../ac/man/bioinf/util/SwingWorker$ThreadVar.class | Bin 0 -> 511 bytes
classes/uk/ac/man/bioinf/util/SwingWorker.class | Bin 0 -> 1810 bytes
debian/README.Debian | 6 -
debian/changelog | 9 -
debian/compat | 1 -
debian/control | 22 -
debian/copyright | 32 -
debian/docs | 1 -
debian/patches/ant.patch | 265 -
debian/patches/application.patch | 52 -
debian/patches/series | 3 -
debian/rules | 27 -
debian/source/format | 1 -
debian/watch | 3 -
doc/ASL | 58 +
doc/AUTHORS | 15 +
doc/CINEMA | 13 +
doc/EXTENDING_CINEMA | 17 +
doc/INSTALL | 106 +
doc/LGPL | 311 +
doc/LICENSING | 39 +
doc/cinema-changes.html | 454 ++
doc/cinema-module/cinema-module.aux | 51 +
doc/cinema-module/cinema-module.dvi | Bin 0 -> 41152 bytes
doc/cinema-module/cinema-module.log | 244 +
doc/cinema-module/cinema-module.pdf | Bin 0 -> 50450 bytes
doc/cinema-module/cinema-module.tex | 540 ++
doc/cinema-module/cinema-module.wiz | 0
doc/cinema-module/cinema-module/WARNINGS | 6 +
doc/cinema-module/cinema-module/cinema-module.css | 30 +
doc/cinema-module/cinema-module/cinema-module.html | 110 +
doc/cinema-module/cinema-module/footnode.html | 107 +
doc/cinema-module/cinema-module/index.html | 110 +
doc/cinema-module/cinema-module/internals.pl | 46 +
doc/cinema-module/cinema-module/labels.pl | 137 +
doc/cinema-module/cinema-module/node1.html | 84 +
doc/cinema-module/cinema-module/node10.html | 138 +
doc/cinema-module/cinema-module/node11.html | 225 +
doc/cinema-module/cinema-module/node12.html | 122 +
doc/cinema-module/cinema-module/node13.html | 74 +
doc/cinema-module/cinema-module/node2.html | 83 +
doc/cinema-module/cinema-module/node3.html | 157 +
doc/cinema-module/cinema-module/node4.html | 75 +
doc/cinema-module/cinema-module/node5.html | 197 +
doc/cinema-module/cinema-module/node6.html | 81 +
doc/cinema-module/cinema-module/node7.html | 86 +
doc/cinema-module/cinema-module/node8.html | 130 +
doc/cinema-module/cinema-module/node9.html | 154 +
doc/cinema-module/listings.perl | 12 +
doc/cinema-module/missfont.log | 84 +
doc/javadoc/allclasses-frame.html | 777 ++
doc/javadoc/allclasses-noframe.html | 777 ++
doc/javadoc/constant-values.html | 519 ++
doc/javadoc/deprecated-list.html | 121 +
doc/javadoc/help-doc.html | 176 +
doc/javadoc/index-all.html | 8309 ++++++++++++++++++++
doc/javadoc/index.html | 25 +
doc/javadoc/overview-frame.html | 134 +
doc/javadoc/overview-summary.html | 341 +
doc/javadoc/overview-tree.html | 517 ++
doc/javadoc/package-list | 47 +
doc/javadoc/packages.html | 26 +
doc/javadoc/serialized-form.html | 2735 +++++++
doc/javadoc/stylesheet.css | 29 +
doc/javadoc/uk/ac/man/bioinf/Y.html | 223 +
.../analysis/consensus/ConsensusCalculator.html | 252 +
.../analysis/consensus/ConsensusIdentifier.html | 286 +
.../analysis/consensus/ConsensusSequence.html | 300 +
.../consensus/DefaultConsensusSequence.html | 849 ++
.../analysis/consensus/PercentageIDConsensus.html | 336 +
.../consensus/ThreadedConsensusSequence.html | 410 +
.../bioinf/analysis/consensus/package-frame.html | 51 +
.../bioinf/analysis/consensus/package-summary.html | 182 +
.../bioinf/analysis/consensus/package-tree.html | 169 +
.../analysis/misc/PercentageIDCalculator.html | 383 +
.../misc/PercentageIDCalculatorManager.html | 271 +
.../ac/man/bioinf/analysis/misc/package-frame.html | 34 +
.../man/bioinf/analysis/misc/package-summary.html | 144 +
.../ac/man/bioinf/analysis/misc/package-tree.html | 133 +
.../regexp/GappedSequenceCharacterIterator.html | 311 +
.../analysis/regexp/SequenceCharacterIterator.html | 312 +
.../man/bioinf/analysis/regexp/package-frame.html | 34 +
.../bioinf/analysis/regexp/package-summary.html | 144 +
.../man/bioinf/analysis/regexp/package-tree.html | 132 +
.../uk/ac/man/bioinf/apps/cinema/Cinema.html | 318 +
.../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html | 391 +
.../bioinf/apps/cinema/CinemaBootIdentifier.html | 292 +
.../ac/man/bioinf/apps/cinema/CinemaGuiModule.html | 518 ++
.../uk/ac/man/bioinf/apps/cinema/CinemaModule.html | 753 ++
.../apps/cinema/CinemaModuleFactoryInstance.html | 277 +
.../man/bioinf/apps/cinema/CinemaProperties.html | 262 +
.../uk/ac/man/bioinf/apps/cinema/CinemaShared.html | 304 +
.../bioinf/apps/cinema/CinemaXMLParserFactory.html | 258 +
.../cinema/color/AminoAcidColorMapMetaData.html | 375 +
.../apps/cinema/color/CinemaColorFactory.html | 466 ++
.../apps/cinema/color/CinemaColorIdentifier.html | 292 +
.../apps/cinema/color/CinemaColorSelector.html | 403 +
.../bioinf/apps/cinema/color/ColorMapMetaData.html | 293 +
.../cinema/color/ColormapColorMapMetaData.html | 374 +
.../apps/cinema/color/DefaultColorMapMetaData.html | 374 +
.../apps/cinema/color/GrayScaleVariance.html | 344 +
.../InstancePerAlignmentColorMapMetaData.html | 311 +
.../apps/cinema/color/IntenseColorMapMetaData.html | 374 +
.../apps/cinema/color/Js_TestColorMapMetaData.html | 374 +
.../apps/cinema/color/NullColorMapMetaData.html | 344 +
.../cinema/color/PedanticColorMapMetaData.html | 374 +
.../PercentageIDVarianceColorMapMetaData.html | 344 +
.../apps/cinema/color/TaylorColorMapMetaData.html | 396 +
...readedPercentageIDVarianceColorMapMetaData.html | 344 +
.../cinema/color/VariableColorMapMetaData.html | 374 +
.../cinema/color/VariationsColorMapMetaData.html | 374 +
.../apps/cinema/color/WhiteColorMapMetaData.html | 344 +
.../apps/cinema/color/ZenecaColorMapMetaData.html | 374 +
.../bioinf/apps/cinema/color/package-frame.html | 79 +
.../bioinf/apps/cinema/color/package-summary.html | 270 +
.../man/bioinf/apps/cinema/color/package-tree.html | 168 +
.../apps/cinema/consensus/CinemaConsensus.html | 431 +
.../CinemaConsensusCalculatorMetaData.html | 252 +
.../cinema/consensus/CinemaConsensusDisplay.html | 453 ++
.../consensus/CinemaConsensusIdentifier.html | 292 +
.../PercentageIDConsensusCalculatorMetaData.html | 349 +
...dedPercentageIDConsensusCalculatorMetaData.html | 313 +
.../apps/cinema/consensus/package-frame.html | 51 +
.../apps/cinema/consensus/package-summary.html | 179 +
.../bioinf/apps/cinema/consensus/package-tree.html | 155 +
.../cinema/core/AlignmentToListCellRenderer.html | 434 +
.../apps/cinema/core/AlignmentToListModel.html | 345 +
.../apps/cinema/core/CinemaActionProvider.html | 214 +
.../man/bioinf/apps/cinema/core/CinemaCoreGui.html | 714 ++
.../apps/cinema/core/CinemaCoreIdentifier.html | 328 +
.../bioinf/apps/cinema/core/CinemaCoreView.html | 733 ++
.../cinema/core/CinemaFramedActionProvider.html | 214 +
.../ac/man/bioinf/apps/cinema/core/CinemaGo.html | 338 +
.../bioinf/apps/cinema/core/CinemaMenuSystem.html | 360 +
.../cinema/core/CinemaModuleCoreIdentifier.html | 292 +
.../apps/cinema/core/CinemaSequenceMenu.html | 388 +
.../apps/cinema/core/CinemaSystemEvents.html | 413 +
.../apps/cinema/core/VersionInformation.html | 348 +
.../man/bioinf/apps/cinema/core/package-frame.html | 65 +
.../bioinf/apps/cinema/core/package-summary.html | 228 +
.../man/bioinf/apps/cinema/core/package-tree.html | 171 +
.../apps/cinema/core/test/CinemaTestLaunch.html | 294 +
.../cinema/core/test/CinemaTestModuleLaunch.html | 254 +
.../apps/cinema/core/test/package-frame.html | 34 +
.../apps/cinema/core/test/package-summary.html | 144 +
.../bioinf/apps/cinema/core/test/package-tree.html | 132 +
.../apps/cinema/group/CinemaAnchorManager.html | 372 +
.../man/bioinf/apps/cinema/group/CinemaGroup.html | 362 +
.../bioinf/apps/cinema/group/CinemaGroupFrame.html | 528 ++
.../apps/cinema/group/CinemaGroupIdentifier.html | 274 +
.../apps/cinema/group/CinemaGroupManager.html | 642 ++
.../apps/cinema/group/CinemaGroupModule.html | 553 ++
.../bioinf/apps/cinema/group/package-frame.html | 42 +
.../bioinf/apps/cinema/group/package-summary.html | 174 +
.../man/bioinf/apps/cinema/group/package-tree.html | 170 +
.../apps/cinema/io/AbstractSequenceInput.html | 540 ++
...bstractSequenceInputParserExceptionHandler.html | 330 +
.../apps/cinema/io/AbstractSequenceOutput.html | 549 ++
.../io/AbstractSequenceParserExceptionHandler.html | 330 +
.../apps/cinema/io/CinemaCommandLineParser.html | 377 +
.../io/CinemaCommandLineParserIdentifier.html | 274 +
.../bioinf/apps/cinema/io/FileSequenceInput.html | 419 +
.../FileSequenceInputParserExceptionHandler.html | 270 +
.../bioinf/apps/cinema/io/FileSequenceOutput.html | 379 +
.../io/FileSequenceParserExceptionHandler.html | 270 +
.../cinema/io/SequenceInputModuleIdentifier.html | 294 +
.../cinema/io/SequenceOutputModuleIdentifier.html | 292 +
.../man/bioinf/apps/cinema/io/package-frame.html | 54 +
.../man/bioinf/apps/cinema/io/package-summary.html | 194 +
.../ac/man/bioinf/apps/cinema/io/package-tree.html | 158 +
.../bioinf/apps/cinema/motif/CinemaMotifFrame.html | 582 ++
.../apps/cinema/motif/CinemaMotifIdentifier.html | 274 +
.../apps/cinema/motif/CinemaMotifModule.html | 373 +
.../cinema/motif/NamedAlignmentSelectionModel.html | 753 ++
.../bioinf/apps/cinema/motif/package-frame.html | 38 +
.../bioinf/apps/cinema/motif/package-summary.html | 157 +
.../man/bioinf/apps/cinema/motif/package-tree.html | 161 +
.../ac/man/bioinf/apps/cinema/package-frame.html | 48 +
.../ac/man/bioinf/apps/cinema/package-summary.html | 191 +
.../uk/ac/man/bioinf/apps/cinema/package-tree.html | 152 +
.../apps/cinema/resources/CinemaResources.html | 372 +
.../apps/cinema/resources/package-frame.html | 32 +
.../apps/cinema/resources/package-summary.html | 138 +
.../bioinf/apps/cinema/resources/package-tree.html | 132 +
.../apps/cinema/shared/CinemaDebug.DebugImpl.html | 285 +
.../man/bioinf/apps/cinema/shared/CinemaDebug.html | 394 +
.../apps/cinema/shared/CinemaSharedIdentifier.html | 310 +
.../apps/cinema/shared/CinemaSharedQuitExit.html | 289 +
.../bioinf/apps/cinema/shared/CinemaSplash.html | 341 +
.../bioinf/apps/cinema/shared/package-frame.html | 38 +
.../bioinf/apps/cinema/shared/package-summary.html | 158 +
.../bioinf/apps/cinema/shared/package-tree.html | 148 +
.../apps/cinema/utils/CinemaAlignmentFrame.html | 708 ++
.../apps/cinema/utils/CinemaDebug.DebugImpl.html | 285 +
.../man/bioinf/apps/cinema/utils/CinemaDebug.html | 394 +
.../CinemaFileOptionableExceptionHandler.html | 398 +
.../apps/cinema/utils/CinemaFilePersist.html | 373 +
.../bioinf/apps/cinema/utils/CinemaInvoker.html | 362 +
.../apps/cinema/utils/CinemaMenuBuilder.html | 358 +
.../utils/CinemaMultipleConsensusViewer.html | 489 ++
.../bioinf/apps/cinema/utils/CinemaPersist.html | 316 +
.../man/bioinf/apps/cinema/utils/CinemaRegexp.html | 318 +
.../apps/cinema/utils/CinemaResizeElements.html | 339 +
.../apps/cinema/utils/CinemaSlaveViewerModule.html | 325 +
.../apps/cinema/utils/CinemaStatusInformation.html | 355 +
.../apps/cinema/utils/CinemaUtilityIdentifier.html | 418 +
.../utils/ConsensusPercentageIDColorMap.html | 344 +
.../bioinf/apps/cinema/utils/package-frame.html | 58 +
.../bioinf/apps/cinema/utils/package-summary.html | 227 +
.../man/bioinf/apps/cinema/utils/package-tree.html | 176 +
.../apps/commandline/CalculatePercentageID.html | 254 +
.../CheckMotifLocationAgainstPrints.html | 343 +
.../apps/commandline/GappedSequenceSearch.html | 256 +
.../bioinf/apps/commandline/SequenceSearch.html | 256 +
.../man/bioinf/apps/commandline/package-frame.html | 38 +
.../bioinf/apps/commandline/package-summary.html | 158 +
.../man/bioinf/apps/commandline/package-tree.html | 132 +
.../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html | 346 +
.../uk/ac/man/bioinf/apps/invoker/Invoker.html | 439 ++
.../InvokerInternalEventQueueException.html | 271 +
.../bioinf/apps/invoker/InvokerInternalQueue.html | 578 ++
.../invoker/InvokerInternalQueueException.html | 238 +
.../bioinf/apps/invoker/InvokerThreadManager.html | 304 +
.../ac/man/bioinf/apps/invoker/package-frame.html | 51 +
.../man/bioinf/apps/invoker/package-summary.html | 182 +
.../ac/man/bioinf/apps/invoker/package-tree.html | 143 +
.../apps/optionable/FileSaveableOptions.html | 321 +
.../bioinf/apps/optionable/NullOptionHandler.html | 315 +
.../man/bioinf/apps/optionable/OptionHandler.html | 269 +
.../ac/man/bioinf/apps/optionable/Optionable.html | 324 +
.../optionable/OptionableExceptionHandler.html | 333 +
.../OptionableSourceNotFoundException.html | 252 +
.../apps/optionable/OptionableStateException.html | 239 +
.../bioinf/apps/optionable/SaveableOptions.html | 497 ++
.../man/bioinf/apps/optionable/package-frame.html | 64 +
.../bioinf/apps/optionable/package-summary.html | 207 +
.../man/bioinf/apps/optionable/package-tree.html | 148 +
.../man/bioinf/apps/systemevents/SystemEvent.html | 287 +
.../apps/systemevents/SystemEventOption.html | 262 +
.../apps/systemevents/SystemEventProducer.html | 234 +
.../apps/systemevents/SystemEventSupport.html | 334 +
.../bioinf/apps/systemevents/SystemListener.html | 348 +
.../apps/systemevents/SystemVetoException.html | 270 +
.../bioinf/apps/systemevents/package-frame.html | 60 +
.../bioinf/apps/systemevents/package-summary.html | 191 +
.../man/bioinf/apps/systemevents/package-tree.html | 148 +
.../uk/ac/man/bioinf/apps/xml/ConfigNode.html | 373 +
.../ac/man/bioinf/apps/xml/DefaultXMLParser.html | 258 +
.../ac/man/bioinf/apps/xml/XMLBootIdentifier.html | 274 +
.../bioinf/apps/xml/XMLBootModule.MiniStack.html | 280 +
.../uk/ac/man/bioinf/apps/xml/XMLBootModule.html | 874 ++
.../man/bioinf/apps/xml/XMLBootParserListener.html | 574 ++
.../uk/ac/man/bioinf/apps/xml/XMLModule.html | 290 +
.../ac/man/bioinf/apps/xml/XMLParserFactory.html | 214 +
.../uk/ac/man/bioinf/apps/xml/package-frame.html | 53 +
.../uk/ac/man/bioinf/apps/xml/package-summary.html | 189 +
.../uk/ac/man/bioinf/apps/xml/package-tree.html | 146 +
.../man/bioinf/apps/xml/test/XMLLoadingTest.html | 330 +
.../ac/man/bioinf/apps/xml/test/XMLStartTest.html | 254 +
.../ac/man/bioinf/apps/xml/test/package-frame.html | 34 +
.../man/bioinf/apps/xml/test/package-summary.html | 144 +
.../ac/man/bioinf/apps/xml/test/package-tree.html | 135 +
.../database/fetch/ExpasySequenceRetriever.html | 358 +
.../database/fetch/FetchSequenceBySwissProtID.html | 220 +
.../bioinf/database/fetch/SequenceRetriever.html | 281 +
.../man/bioinf/database/fetch/package-frame.html | 45 +
.../man/bioinf/database/fetch/package-summary.html | 160 +
.../ac/man/bioinf/database/fetch/package-tree.html | 138 +
.../uk/ac/man/bioinf/debug/AbstractDebug.html | 487 ++
doc/javadoc/uk/ac/man/bioinf/debug/Debug.html | 560 ++
.../uk/ac/man/bioinf/debug/DebugInterface.html | 413 +
.../uk/ac/man/bioinf/debug/DebugMultiplexer.html | 524 ++
.../uk/ac/man/bioinf/debug/DefaultDebug.html | 296 +
.../uk/ac/man/bioinf/debug/DefaultFileDebug.html | 296 +
doc/javadoc/uk/ac/man/bioinf/debug/NullDebug.html | 297 +
.../uk/ac/man/bioinf/debug/package-frame.html | 53 +
.../uk/ac/man/bioinf/debug/package-summary.html | 188 +
.../uk/ac/man/bioinf/debug/package-tree.html | 141 +
.../uk/ac/man/bioinf/gui/color/ColorGenerator.html | 306 +
.../uk/ac/man/bioinf/gui/color/ColorList.html | 413 +
.../uk/ac/man/bioinf/gui/color/ColorMap.html | 250 +
.../ac/man/bioinf/gui/color/ColorMapException.html | 238 +
.../uk/ac/man/bioinf/gui/color/ColorStore.html | 194 +
.../man/bioinf/gui/color/DoubleArrayColorMap.html | 303 +
.../gui/color/IndividualElementColorMap.html | 300 +
.../gui/color/PercentIDVarianceColorMap.html | 364 +
.../uk/ac/man/bioinf/gui/color/SingleColorMap.html | 313 +
.../man/bioinf/gui/color/ThreadableColorMap.html | 234 +
.../ac/man/bioinf/gui/color/ThreadedColorMap.html | 495 ++
.../uk/ac/man/bioinf/gui/color/package-frame.html | 70 +
.../ac/man/bioinf/gui/color/package-summary.html | 228 +
.../uk/ac/man/bioinf/gui/color/package-tree.html | 151 +
.../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html | 1054 +++
...ppingListBasicUI.SwappingMouseInputHandler.html | 302 +
.../man/bioinf/gui/misc/SwappingListBasicUI.html | 368 +
.../uk/ac/man/bioinf/gui/misc/package-frame.html | 34 +
.../uk/ac/man/bioinf/gui/misc/package-summary.html | 143 +
.../uk/ac/man/bioinf/gui/misc/package-tree.html | 144 +
.../bioinf/gui/optionable/OptionableJFrame.html | 788 ++
.../gui/optionable/OptionableJSplitPane.html | 634 ++
.../man/bioinf/gui/optionable/package-frame.html | 34 +
.../man/bioinf/gui/optionable/package-summary.html | 145 +
.../ac/man/bioinf/gui/optionable/package-tree.html | 154 +
.../ac/man/bioinf/gui/util/ApplicationFrame.html | 852 ++
.../ac/man/bioinf/gui/util/PopUpHtmlDisplay.html | 239 +
.../uk/ac/man/bioinf/gui/util/TripletPanel.html | 489 ++
.../ac/man/bioinf/gui/util/forms/DecimalField.html | 481 ++
.../bioinf/gui/util/forms/FormattedDocument.html | 370 +
.../util/forms/IntegerField.IntegerDocument.html | 330 +
.../ac/man/bioinf/gui/util/forms/IntegerField.html | 499 ++
.../man/bioinf/gui/util/forms/PasswordDialog.html | 533 ++
.../man/bioinf/gui/util/forms/ValidatedForm.html | 776 ++
.../WholeNumberField.WholeNumberDocument.html | 330 +
.../bioinf/gui/util/forms/WholeNumberField.html | 467 ++
.../man/bioinf/gui/util/forms/package-frame.html | 42 +
.../man/bioinf/gui/util/forms/package-summary.html | 154 +
.../ac/man/bioinf/gui/util/forms/package-tree.html | 154 +
.../uk/ac/man/bioinf/gui/util/package-frame.html | 36 +
.../uk/ac/man/bioinf/gui/util/package-summary.html | 142 +
.../uk/ac/man/bioinf/gui/util/package-tree.html | 152 +
.../bioinf/gui/viewer/AlignmentSelectionModel.html | 469 ++
.../gui/viewer/AlignmentSelectionRenderer.html | 226 +
.../gui/viewer/AlignmentViewerCellRenderer.html | 237 +
.../BorderFastAlignmentViewerCellRenderer.html | 293 +
.../bioinf/gui/viewer/ButtonViewerPopupMenu.html | 404 +
.../ColorFastAlignmentViewerCellRenderer.html | 293 +
.../CursorLessFastAlignmentViewerCellRenderer.html | 298 +
.../viewer/DefaultAlignmentSelectionRenderer.html | 270 +
.../viewer/DefaultAlignmentViewerCellRenderer.html | 415 +
.../DefaultFastAlignmentViewerCellRenderer.html | 318 +
.../bioinf/gui/viewer/DefaultSequenceCursor.html | 388 +
.../viewer/FastAlignmentViewerCellRenderer.html | 255 +
.../uk/ac/man/bioinf/gui/viewer/Install.html | 289 +
.../gui/viewer/InvertedScrollPaneLayout.html | 310 +
.../bioinf/gui/viewer/JAlignmentButtonPanel.html | 692 ++
.../ac/man/bioinf/gui/viewer/JAlignmentRuler.html | 671 ++
.../ac/man/bioinf/gui/viewer/JAlignmentViewer.html | 2037 +++++
.../man/bioinf/gui/viewer/JChangedScrollPane.html | 386 +
.../man/bioinf/gui/viewer/JLayableScrollPane.html | 391 +
...MultiplexerFastAlignmentViewerCellRenderer.html | 344 +
.../gui/viewer/NullAlignmentSelectionModel.html | 569 ++
.../bioinf/gui/viewer/PrintableAlignmentPanel.html | 344 +
.../gui/viewer/PrintableJAlignmentViewer.html | 516 ++
.../man/bioinf/gui/viewer/ReadonlyException.html | 319 +
.../ac/man/bioinf/gui/viewer/SequenceCursor.html | 323 +
.../gui/viewer/SingleAlignmentSelectionModel.html | 549 ++
.../TextFastAlignmentViewerCellRenderer.html | 293 +
.../gui/viewer/event/AlignmentSelectionEvent.html | 327 +
.../viewer/event/AlignmentSelectionListener.html | 220 +
.../event/AlignmentSelectionListenerSupport.html | 290 +
.../gui/viewer/event/ChangeListenerSupport.html | 290 +
.../man/bioinf/gui/viewer/event/package-frame.html | 47 +
.../bioinf/gui/viewer/event/package-summary.html | 168 +
.../man/bioinf/gui/viewer/event/package-tree.html | 142 +
.../uk/ac/man/bioinf/gui/viewer/package-frame.html | 102 +
.../ac/man/bioinf/gui/viewer/package-summary.html | 341 +
.../uk/ac/man/bioinf/gui/viewer/package-tree.html | 189 +
.../bioinf/gui/viewer/plaf/AlignmentRulerUI.html | 231 +
.../bioinf/gui/viewer/plaf/AlignmentViewerUI.html | 346 +
.../gui/viewer/plaf/BasicAlignmentRulerUI.html | 508 ++
.../plaf/BasicAlignmentViewerUI.KeyScroller.html | 335 +
.../plaf/BasicAlignmentViewerUI.PointListener.html | 248 +
.../BasicAlignmentViewerUI.SelectionClearer.html | 248 +
.../BasicAlignmentViewerUI.SelectionToggler.html | 248 +
.../gui/viewer/plaf/BasicAlignmentViewerUI.html | 1014 +++
.../gui/viewer/plaf/MetalAlignmentViewerUI.html | 272 +
.../man/bioinf/gui/viewer/plaf/package-frame.html | 40 +
.../bioinf/gui/viewer/plaf/package-summary.html | 165 +
.../man/bioinf/gui/viewer/plaf/package-tree.html | 147 +
.../gui/viewer/test/AlignmentViewerTest.html | 426 +
.../bioinf/gui/viewer/test/BasicWindowMonitor.html | 256 +
.../bioinf/gui/viewer/test/ButtonPanelTest.html | 282 +
.../viewer/test/CellRendererPaneReplacement.html | 373 +
.../gui/viewer/test/SingleSelectionModelTest.html | 252 +
.../man/bioinf/gui/viewer/test/SliderExample.html | 365 +
.../man/bioinf/gui/viewer/test/package-frame.html | 42 +
.../bioinf/gui/viewer/test/package-summary.html | 166 +
.../man/bioinf/gui/viewer/test/package-tree.html | 159 +
.../uk/ac/man/bioinf/io/AlignmentInputParser.html | 281 +
.../uk/ac/man/bioinf/io/AlignmentOutputParser.html | 257 +
.../bioinf/io/DefaultParserExceptionHandler.html | 261 +
.../io/InvalidSequenceTypeParserException.html | 329 +
.../uk/ac/man/bioinf/io/NarrowedInputStream.html | 302 +
.../man/bioinf/io/NullParserExceptionHandler.html | 290 +
.../uk/ac/man/bioinf/io/ParserException.html | 390 +
.../ac/man/bioinf/io/ParserExceptionHandler.html | 216 +
.../uk/ac/man/bioinf/io/SequenceInputParser.html | 238 +
.../ac/man/bioinf/io/SequenceWriterException.html | 250 +
.../ac/man/bioinf/io/UnknownElementException.html | 319 +
doc/javadoc/uk/ac/man/bioinf/io/package-frame.html | 70 +
.../uk/ac/man/bioinf/io/package-summary.html | 207 +
doc/javadoc/uk/ac/man/bioinf/io/package-tree.html | 150 +
.../AbstractProteinAlignmentInputParser.html | 274 +
.../AbstractProteinSequenceInputParser.html | 323 +
.../man/bioinf/io/parsers/FastaSequenceParser.html | 314 +
.../ac/man/bioinf/io/parsers/MotProteinParser.html | 303 +
.../io/parsers/PIRProteinAlignmentParser.html | 372 +
.../uk/ac/man/bioinf/io/parsers/package-frame.html | 40 +
.../ac/man/bioinf/io/parsers/package-summary.html | 159 +
.../uk/ac/man/bioinf/io/parsers/package-tree.html | 140 +
.../man/bioinf/io/test/AlignmentParserIOTest.html | 252 +
.../bioinf/io/test/AlignmentParserInputTest.html | 252 +
.../uk/ac/man/bioinf/io/test/package-frame.html | 34 +
.../uk/ac/man/bioinf/io/test/package-summary.html | 144 +
.../uk/ac/man/bioinf/io/test/package-tree.html | 132 +
.../module/AbstractEnumeratedModuleIdentifier.html | 424 +
.../ac/man/bioinf/module/DefaultModuleContext.html | 298 +
.../module/DefaultModuleFactoryInstance.html | 631 ++
.../man/bioinf/module/GenericModuleIdentifier.html | 318 +
doc/javadoc/uk/ac/man/bioinf/module/Module.html | 713 ++
.../uk/ac/man/bioinf/module/ModuleContext.html | 437 +
.../uk/ac/man/bioinf/module/ModuleException.html | 350 +
.../ac/man/bioinf/module/ModuleExceptionType.html | 342 +
.../man/bioinf/module/ModuleFactoryInstance.html | 471 ++
.../uk/ac/man/bioinf/module/ModuleIdentifier.html | 262 +
.../ac/man/bioinf/module/ModuleIdentifierList.html | 454 ++
.../uk/ac/man/bioinf/module/ModuleList.html | 453 ++
.../man/bioinf/module/ModuleStorageStructure.html | 478 ++
.../ac/man/bioinf/module/NoSuchRequiredModule.html | 270 +
.../uk/ac/man/bioinf/module/NullModuleFactory.html | 578 ++
.../uk/ac/man/bioinf/module/package-frame.html | 78 +
.../uk/ac/man/bioinf/module/package-summary.html | 245 +
.../uk/ac/man/bioinf/module/package-tree.html | 152 +
doc/javadoc/uk/ac/man/bioinf/package-frame.html | 32 +
doc/javadoc/uk/ac/man/bioinf/package-summary.html | 137 +
doc/javadoc/uk/ac/man/bioinf/package-tree.html | 132 +
.../bioinf/sequence/AbstractEditableSequence.html | 550 ++
.../bioinf/sequence/AbstractMutableSequence.html | 436 +
.../ac/man/bioinf/sequence/AbstractSequence.html | 484 ++
.../sequence/ComplexEditableGappedSequence.html | 236 +
.../bioinf/sequence/DefaultEditableSequence.html | 506 ++
.../uk/ac/man/bioinf/sequence/DefaultSequence.html | 385 +
.../ac/man/bioinf/sequence/EditableSequence.html | 420 +
doc/javadoc/uk/ac/man/bioinf/sequence/Element.html | 225 +
.../uk/ac/man/bioinf/sequence/EmptySequence.html | 437 +
.../sequence/InvalidSequenceTypeException.html | 240 +
.../uk/ac/man/bioinf/sequence/MutableSequence.html | 219 +
.../sequence/NoSuchSequenceElementException.html | 286 +
doc/javadoc/uk/ac/man/bioinf/sequence/Residue.html | 198 +
.../uk/ac/man/bioinf/sequence/Sequence.html | 391 +
.../ac/man/bioinf/sequence/SequenceException.html | 238 +
.../uk/ac/man/bioinf/sequence/SequenceFactory.html | 364 +
.../uk/ac/man/bioinf/sequence/SequenceType.html | 413 +
.../uk/ac/man/bioinf/sequence/Sequences.html | 667 ++
.../sequence/alignment/AbstractGappedSequence.html | 563 ++
.../alignment/AbstractSequenceAlignment.html | 807 ++
.../bioinf/sequence/alignment/AlignmentColumn.html | 363 +
.../sequence/alignment/DefaultGappedSequence.html | 777 ++
.../alignment/DefaultSequenceAlignment.html | 673 ++
.../sequence/alignment/EmptyGappedSequence.html | 871 ++
.../sequence/alignment/EmptySequenceAlignment.html | 855 ++
.../uk/ac/man/bioinf/sequence/alignment/Gap.html | 307 +
.../bioinf/sequence/alignment/GappedSequence.html | 556 ++
.../alignment/NoGapAtThisPositionException.html | 328 +
.../alignment/NoSuchSequenceException.html | 287 +
.../sequence/alignment/SequenceAlignment.html | 554 ++
.../alignment/SingleSequenceAlignment.html | 300 +
.../sequence/alignment/event/AlignmentEvent.html | 363 +
.../alignment/event/AlignmentEventProvider.html | 284 +
.../alignment/event/AlignmentEventType.html | 353 +
.../alignment/event/AlignmentListener.html | 225 +
.../alignment/event/AlignmentListenerSupport.html | 368 +
.../alignment/event/AlignmentVetoException.html | 276 +
.../alignment/event/VetoableAlignmentEvent.html | 286 +
.../alignment/event/VetoableAlignmentListener.html | 240 +
.../sequence/alignment/event/package-frame.html | 64 +
.../sequence/alignment/event/package-summary.html | 205 +
.../sequence/alignment/event/package-tree.html | 151 +
.../bioinf/sequence/alignment/package-frame.html | 74 +
.../bioinf/sequence/alignment/package-summary.html | 237 +
.../bioinf/sequence/alignment/package-tree.html | 185 +
.../sequence/complex/AbstractComplexSequence.html | 566 ++
.../complex/AbstractComplexSequenceType.html | 408 +
.../bioinf/sequence/complex/ComplexElement.html | 273 +
.../sequence/complex/ComplexElementFactory.html | 376 +
.../complex/ComplexElementFactoryInterface.html | 274 +
.../bioinf/sequence/complex/ComplexSequence.html | 355 +
.../sequence/complex/ComplexSequenceType.html | 317 +
.../sequence/complex/DefaultComplexElement.html | 346 +
.../sequence/complex/DefaultComplexSequence.html | 450 ++
.../complex/DefaultComplexSequenceType.html | 604 ++
.../complex/DefaultGappedComplexSequence.html | 910 +++
.../sequence/complex/GappedComplexSequence.html | 231 +
.../complex/HardModificationSetFactory.html | 326 +
.../IllegalDuplicateModificationException.html | 238 +
.../man/bioinf/sequence/complex/Methylation.html | 240 +
.../man/bioinf/sequence/complex/Modification.html | 233 +
.../sequence/complex/ModificationFactory.html | 273 +
.../complex/ModificationSetFactoryInterface.html | 273 +
.../complex/NoSuchModificationException.html | 238 +
.../sequence/complex/SingletonModification.html | 258 +
.../complex/WeakModificationSetFactory.html | 326 +
.../man/bioinf/sequence/complex/package-frame.html | 90 +
.../bioinf/sequence/complex/package-summary.html | 314 +
.../man/bioinf/sequence/complex/package-tree.html | 192 +
.../man/bioinf/sequence/event/SequenceEvent.html | 387 +
.../sequence/event/SequenceEventProvider.html | 284 +
.../bioinf/sequence/event/SequenceEventType.html | 354 +
.../bioinf/sequence/event/SequenceListener.html | 224 +
.../sequence/event/SequenceListenerSupport.html | 391 +
.../sequence/event/SequenceVetoException.html | 276 +
.../sequence/event/VetoableSequenceEvent.html | 285 +
.../sequence/event/VetoableSequenceListener.html | 246 +
.../man/bioinf/sequence/event/package-frame.html | 64 +
.../man/bioinf/sequence/event/package-summary.html | 205 +
.../ac/man/bioinf/sequence/event/package-tree.html | 153 +
.../sequence/geom/SequenceAlignmentDimension.html | 427 +
.../sequence/geom/SequenceAlignmentPoint.html | 571 ++
.../sequence/geom/SequenceAlignmentRectangle.html | 830 ++
.../sequence/geom/SequenceAlignmentShape.html | 220 +
.../ac/man/bioinf/sequence/geom/package-frame.html | 47 +
.../man/bioinf/sequence/geom/package-summary.html | 165 +
.../ac/man/bioinf/sequence/geom/package-tree.html | 139 +
.../group/AbstractGappedSequenceGroup.html | 278 +
.../sequence/group/DefaultGappedSequenceGroup.html | 444 ++
.../bioinf/sequence/group/GappedSequenceGroup.html | 237 +
.../sequence/group/GroupSequenceAlignment.html | 1071 +++
.../man/bioinf/sequence/group/SequenceGroup.html | 355 +
.../man/bioinf/sequence/group/package-frame.html | 49 +
.../man/bioinf/sequence/group/package-summary.html | 175 +
.../ac/man/bioinf/sequence/group/package-tree.html | 143 +
.../sequence/identifier/AbstractIdentifier.html | 300 +
.../sequence/identifier/DatabaseIdentifier.html | 313 +
.../man/bioinf/sequence/identifier/FileSource.html | 284 +
.../bioinf/sequence/identifier/Identifiable.html | 217 +
.../man/bioinf/sequence/identifier/Identifier.html | 262 +
.../identifier/MalformedAccessionException.html | 242 +
.../bioinf/sequence/identifier/NoIdentifier.html | 328 +
.../man/bioinf/sequence/identifier/NoSource.html | 262 +
.../bioinf/sequence/identifier/ReaderSource.html | 238 +
.../bioinf/sequence/identifier/SequenceSource.html | 221 +
.../sequence/identifier/SimpleIdentifier.html | 286 +
.../bioinf/sequence/identifier/SimpleSource.html | 266 +
.../ac/man/bioinf/sequence/identifier/Source.html | 221 +
.../sequence/identifier/StreamSequenceSource.html | 294 +
.../sequence/identifier/SwissProtIdentifier.html | 283 +
.../sequence/identifier/URLSequenceSource.html | 293 +
.../bioinf/sequence/identifier/package-frame.html | 80 +
.../sequence/identifier/package-summary.html | 260 +
.../bioinf/sequence/identifier/package-tree.html | 160 +
.../uk/ac/man/bioinf/sequence/package-frame.html | 84 +
.../uk/ac/man/bioinf/sequence/package-summary.html | 288 +
.../uk/ac/man/bioinf/sequence/package-tree.html | 187 +
.../test/ComplexElementAndModificationTest.html | 252 +
.../bioinf/sequence/test/ComplexSequenceTest.html | 273 +
.../bioinf/sequence/test/EditableSequenceTest.html | 271 +
.../bioinf/sequence/test/GappableSequenceTest.html | 271 +
.../bioinf/sequence/test/GappedSequenceTest.html | 254 +
.../sequence/test/SequenceAlignmentTest.html | 338 +
.../bioinf/sequence/test/SequenceColumnTest.html | 254 +
.../bioinf/sequence/test/SequenceFactoryTest.html | 252 +
.../ac/man/bioinf/sequence/test/SequencesTest.html | 252 +
.../ac/man/bioinf/sequence/test/package-frame.html | 48 +
.../man/bioinf/sequence/test/package-summary.html | 193 +
.../ac/man/bioinf/sequence/test/package-tree.html | 133 +
.../man/bioinf/sequence/types/AbstractElement.html | 323 +
.../types/AbstractEnumeratedSequenceType.html | 335 +
.../sequence/types/AbstractSequenceType.html | 490 ++
.../uk/ac/man/bioinf/sequence/types/AminoAcid.html | 760 ++
.../man/bioinf/sequence/types/DNANucleotide.html | 394 +
.../ac/man/bioinf/sequence/types/DNAResidue.html | 195 +
.../man/bioinf/sequence/types/DNASequenceType.html | 292 +
.../bioinf/sequence/types/EmptySequenceType.html | 512 ++
.../bioinf/sequence/types/NucleotideResidue.html | 198 +
.../man/bioinf/sequence/types/ProteinResidue.html | 195 +
.../bioinf/sequence/types/ProteinSequenceType.html | 290 +
.../man/bioinf/sequence/types/RNANucleotide.html | 396 +
.../ac/man/bioinf/sequence/types/RNAResidue.html | 195 +
.../man/bioinf/sequence/types/RNASequenceType.html | 317 +
.../man/bioinf/sequence/types/package-frame.html | 67 +
.../man/bioinf/sequence/types/package-summary.html | 234 +
.../ac/man/bioinf/sequence/types/package-tree.html | 156 +
.../util/AbstractEnumeration.ElementIterator.html | 292 +
.../uk/ac/man/bioinf/util/AbstractEnumeration.html | 415 +
.../uk/ac/man/bioinf/util/ArrayManipulation.html | 297 +
doc/javadoc/uk/ac/man/bioinf/util/Changeable.html | 233 +
.../uk/ac/man/bioinf/util/ChangeableEvent.html | 250 +
.../uk/ac/man/bioinf/util/ChangeableListener.html | 211 +
.../man/bioinf/util/ChangeableListenerSupport.html | 293 +
.../uk/ac/man/bioinf/util/CollectionPrinter.html | 271 +
doc/javadoc/uk/ac/man/bioinf/util/Direction.html | 315 +
.../uk/ac/man/bioinf/util/ExceptionHandler.html | 212 +
.../uk/ac/man/bioinf/util/IntArrayList.html | 651 ++
.../ac/man/bioinf/util/PackageResourceAdapter.html | 315 +
.../uk/ac/man/bioinf/util/ResourceAdapter.html | 487 ++
.../util/SequenceAlignmentToChangeableAdaptor.html | 350 +
.../uk/ac/man/bioinf/util/package-frame.html | 67 +
.../uk/ac/man/bioinf/util/package-summary.html | 229 +
.../uk/ac/man/bioinf/util/package-tree.html | 148 +
doc/sequence/alignment.sgml | 136 +
doc/sequence/conclusions.sgml | 19 +
doc/sequence/elementandtype.sgml | 174 +
doc/sequence/implementation.sgml | 172 +
doc/sequence/intro.sgml | 32 +
doc/sequence/requirements.sgml | 197 +
doc/sequence/seqimpl.sgml | 315 +
doc/sequence/sequence.sgml | 74 +
lib/app_support.jar | Bin 0 -> 17154 bytes
lib/cinema.jar | Bin 0 -> 190247 bytes
lib/emboss.jar | Bin 0 -> 22 bytes
lib/ext/gnu-getopt.jar | Bin 0 -> 12530 bytes
lib/ext/jakarta-regexp.jar | Bin 0 -> 29871 bytes
lib/ext/xerces.jar | Bin 0 -> 1867525 bytes
lib/graph.jar | Bin 0 -> 22 bytes
lib/gui.jar | Bin 0 -> 92040 bytes
lib/mxc.jar | Bin 0 -> 25118 bytes
lib/sequence.jar | Bin 0 -> 124579 bytes
lib/src.jar | Bin 0 -> 753592 bytes
lib/util.jar | Bin 0 -> 21613 bytes
src/uk/ac/man/bioinf/Y.java | 47 +
.../analysis/consensus/ConsensusCalculator.java | 78 +
.../analysis/consensus/ConsensusIdentifier.java | 81 +
.../analysis/consensus/ConsensusSequence.java | 70 +
.../consensus/DefaultConsensusSequence.java | 244 +
.../analysis/consensus/PercentageIDConsensus.java | 129 +
.../consensus/ThreadedConsensusSequence.java | 129 +
.../analysis/misc/PercentageIDCalculator.java | 206 +
.../misc/PercentageIDCalculatorManager.java | 84 +
.../regexp/GappedSequenceCharacterIterator.java | 87 +
.../analysis/regexp/SequenceCharacterIterator.java | 90 +
src/uk/ac/man/bioinf/apps/cinema/Cinema.java | 180 +
src/uk/ac/man/bioinf/apps/cinema/CinemaBoot.java | 130 +
.../bioinf/apps/cinema/CinemaBootIdentifier.java | 76 +
.../ac/man/bioinf/apps/cinema/CinemaGuiModule.java | 167 +
src/uk/ac/man/bioinf/apps/cinema/CinemaModule.java | 224 +
.../apps/cinema/CinemaModuleFactoryInstance.java | 93 +
.../man/bioinf/apps/cinema/CinemaProperties.java | 70 +
src/uk/ac/man/bioinf/apps/cinema/CinemaShared.java | 48 +
.../bioinf/apps/cinema/CinemaXMLParserFactory.java | 96 +
src/uk/ac/man/bioinf/apps/cinema/changes.html | 454 ++
.../cinema/color/AminoAcidColorMapMetaData.java | 156 +
.../apps/cinema/color/CinemaColorFactory.java | 170 +
.../apps/cinema/color/CinemaColorIdentifier.java | 77 +
.../apps/cinema/color/CinemaColorSelector.java | 158 +
.../bioinf/apps/cinema/color/ColorMapMetaData.java | 93 +
.../cinema/color/ColormapColorMapMetaData.java | 145 +
.../apps/cinema/color/DefaultColorMapMetaData.java | 145 +
.../apps/cinema/color/GrayScaleVariance.java | 77 +
.../InstancePerAlignmentColorMapMetaData.java | 92 +
.../apps/cinema/color/IntenseColorMapMetaData.java | 145 +
.../apps/cinema/color/Js_TestColorMapMetaData.java | 145 +
.../apps/cinema/color/NullColorMapMetaData.java | 84 +
.../cinema/color/PedanticColorMapMetaData.java | 145 +
.../PercentageIDVarianceColorMapMetaData.java | 102 +
.../apps/cinema/color/TaylorColorMapMetaData.java | 147 +
...readedPercentageIDVarianceColorMapMetaData.java | 119 +
.../cinema/color/VariableColorMapMetaData.java | 145 +
.../cinema/color/VariationsColorMapMetaData.java | 145 +
.../apps/cinema/color/WhiteColorMapMetaData.java | 86 +
.../apps/cinema/color/ZenecaColorMapMetaData.java | 145 +
.../apps/cinema/consensus/CinemaConsensus.java | 191 +
.../CinemaConsensusCalculatorMetaData.java | 67 +
.../cinema/consensus/CinemaConsensusDisplay.java | 287 +
.../consensus/CinemaConsensusIdentifier.java | 75 +
.../PercentageIDConsensusCalculatorMetaData.java | 105 +
...dedPercentageIDConsensusCalculatorMetaData.java | 98 +
.../cinema/core/AlignmentToListCellRenderer.java | 82 +
.../apps/cinema/core/AlignmentToListModel.java | 92 +
.../apps/cinema/core/CinemaActionProvider.java | 58 +
.../man/bioinf/apps/cinema/core/CinemaCoreGui.java | 297 +
.../apps/cinema/core/CinemaCoreIdentifier.java | 92 +
.../bioinf/apps/cinema/core/CinemaCoreView.java | 301 +
.../cinema/core/CinemaFramedActionProvider.java | 60 +
.../ac/man/bioinf/apps/cinema/core/CinemaGo.java | 119 +
.../bioinf/apps/cinema/core/CinemaMenuSystem.java | 104 +
.../cinema/core/CinemaModuleCoreIdentifier.java | 74 +
.../apps/cinema/core/CinemaSequenceMenu.java | 110 +
.../apps/cinema/core/CinemaSystemEvents.java | 133 +
.../apps/cinema/core/VersionInformation.java | 166 +
.../apps/cinema/core/test/CinemaTestLaunch.java | 328 +
.../cinema/core/test/CinemaTestModuleLaunch.java | 82 +
.../apps/cinema/group/CinemaAnchorManager.java | 210 +
.../man/bioinf/apps/cinema/group/CinemaGroup.java | 137 +
.../bioinf/apps/cinema/group/CinemaGroupFrame.java | 487 ++
.../apps/cinema/group/CinemaGroupIdentifier.java | 73 +
.../apps/cinema/group/CinemaGroupManager.java | 278 +
.../apps/cinema/group/CinemaGroupModule.java | 387 +
.../apps/cinema/io/AbstractSequenceInput.java | 284 +
...bstractSequenceInputParserExceptionHandler.java | 103 +
.../apps/cinema/io/AbstractSequenceOutput.java | 188 +
.../io/AbstractSequenceParserExceptionHandler.java | 106 +
.../apps/cinema/io/CinemaCommandLineParser.java | 204 +
.../io/CinemaCommandLineParserIdentifier.java | 73 +
.../bioinf/apps/cinema/io/FileSequenceInput.java | 238 +
.../FileSequenceInputParserExceptionHandler.java | 76 +
.../bioinf/apps/cinema/io/FileSequenceOutput.java | 167 +
.../io/FileSequenceParserExceptionHandler.java | 79 +
.../cinema/io/SequenceInputModuleIdentifier.java | 84 +
.../cinema/io/SequenceOutputModuleIdentifier.java | 78 +
.../bioinf/apps/cinema/motif/CinemaMotifFrame.java | 748 ++
.../apps/cinema/motif/CinemaMotifIdentifier.java | 68 +
.../apps/cinema/motif/CinemaMotifModule.java | 113 +
.../cinema/motif/NamedAlignmentSelectionModel.java | 426 +
.../apps/cinema/resources/CinemaResources.java | 211 +
.../man/bioinf/apps/cinema/resources/MakeCinemaJar | 5 +
.../bioinf/apps/cinema/resources/build-install.xml | 133 +
.../apps/cinema/resources/cinema-calculate.xml | 69 +
.../apps/cinema/resources/cinema-identifiers.xml | 81 +
.../man/bioinf/apps/cinema/resources/cinema-io.xml | 82 +
.../bioinf/apps/cinema/resources/cinema-main.xml | 96 +
.../apps/cinema/resources/cinema-manipulate.xml | 38 +
.../bioinf/apps/cinema/resources/cinema-menu.xml | 117 +
.../bioinf/apps/cinema/resources/cinema-shared.xml | 66 +
.../bioinf/apps/cinema/resources/cinema-view.xml | 99 +
.../ac/man/bioinf/apps/cinema/resources/cinema.jpg | Bin 0 -> 10954 bytes
.../ac/man/bioinf/apps/cinema/resources/cinema.xml | 252 +
.../bioinf/apps/cinema/resources/color-convert.el | 282 +
.../man/bioinf/apps/cinema/resources/manifest.mf | 1 +
.../ac/man/bioinf/apps/cinema/resources/module.dtd | 127 +
.../ac/man/bioinf/apps/cinema/resources/shared.xml | 77 +
.../man/bioinf/apps/cinema/shared/CinemaDebug.java | 328 +
.../apps/cinema/shared/CinemaSharedIdentifier.java | 74 +
.../apps/cinema/shared/CinemaSharedQuitExit.java | 150 +
.../bioinf/apps/cinema/shared/CinemaSplash.java | 138 +
.../apps/cinema/utils/CinemaAlignmentFrame.java | 329 +
.../man/bioinf/apps/cinema/utils/CinemaDebug.java | 324 +
.../CinemaFileOptionableExceptionHandler.java | 139 +
.../apps/cinema/utils/CinemaFilePersist.java | 105 +
.../bioinf/apps/cinema/utils/CinemaInvoker.java | 107 +
.../apps/cinema/utils/CinemaMenuBuilder.java | 181 +
.../utils/CinemaMultipleConsensusViewer.java | 205 +
.../bioinf/apps/cinema/utils/CinemaPersist.java | 75 +
.../man/bioinf/apps/cinema/utils/CinemaRegexp.java | 166 +
.../apps/cinema/utils/CinemaResizeElements.java | 385 +
.../apps/cinema/utils/CinemaSlaveViewerModule.java | 126 +
.../apps/cinema/utils/CinemaStatusInformation.java | 181 +
.../apps/cinema/utils/CinemaUtilityIdentifier.java | 135 +
.../utils/ConsensusPercentageIDColorMap.java | 179 +
.../apps/commandline/CalculatePercentageID.java | 75 +
.../CheckMotifLocationAgainstPrints.java | 282 +
.../apps/commandline/GappedSequenceSearch.java | 100 +
.../bioinf/apps/commandline/SequenceSearch.java | 102 +
src/uk/ac/man/bioinf/apps/invoker/AnonInvoker.java | 105 +
src/uk/ac/man/bioinf/apps/invoker/Invoker.java | 174 +
.../InvokerInternalEventQueueException.java | 70 +
.../bioinf/apps/invoker/InvokerInternalQueue.java | 315 +
.../invoker/InvokerInternalQueueException.java | 61 +
.../bioinf/apps/invoker/InvokerThreadManager.java | 78 +
.../apps/optionable/FileSaveableOptions.java | 155 +
.../bioinf/apps/optionable/NullOptionHandler.java | 81 +
.../man/bioinf/apps/optionable/OptionHandler.java | 110 +
.../ac/man/bioinf/apps/optionable/Optionable.java | 101 +
.../optionable/OptionableExceptionHandler.class | Bin 0 -> 360 bytes
.../optionable/OptionableExceptionHandler.java | 87 +
.../OptionableSourceNotFoundException.class | Bin 0 -> 329 bytes
.../OptionableSourceNotFoundException.java | 48 +
.../apps/optionable/OptionableStateException.java | 66 +
.../bioinf/apps/optionable/SaveableOptions.java | 275 +
.../man/bioinf/apps/systemevents/SystemEvent.java | 88 +
.../apps/systemevents/SystemEventOption.java | 89 +
.../apps/systemevents/SystemEventProducer.java | 65 +
.../apps/systemevents/SystemEventSupport.java | 172 +
.../bioinf/apps/systemevents/SystemListener.java | 132 +
.../apps/systemevents/SystemVetoException.java | 76 +
src/uk/ac/man/bioinf/apps/xml/ConfigNode.java | 131 +
.../ac/man/bioinf/apps/xml/DefaultXMLParser.java | 119 +
.../ac/man/bioinf/apps/xml/XMLBootIdentifier.java | 69 +
src/uk/ac/man/bioinf/apps/xml/XMLBootModule.java | 530 ++
.../man/bioinf/apps/xml/XMLBootParserListener.java | 276 +
src/uk/ac/man/bioinf/apps/xml/XMLModule.java | 94 +
.../ac/man/bioinf/apps/xml/XMLParserFactory.java | 63 +
.../man/bioinf/apps/xml/test/XMLLoadingTest.java | 116 +
.../ac/man/bioinf/apps/xml/test/XMLStartTest.java | 67 +
src/uk/ac/man/bioinf/bin/cinema | 84 +
src/uk/ac/man/bioinf/bin/cinema.cygwin | 81 +
src/uk/ac/man/bioinf/bin/cinema.pl | 78 +
src/uk/ac/man/bioinf/build.xml | 333 +
src/uk/ac/man/bioinf/build/cinema-build.xml | 180 +
src/uk/ac/man/bioinf/build/manifest | 2 +
src/uk/ac/man/bioinf/build/package-list | 59 +
src/uk/ac/man/bioinf/build/project-ext.dtd | 34 +
src/uk/ac/man/bioinf/build/project.dtd | 273 +
.../database/fetch/ExpasySequenceRetriever.java | 115 +
.../database/fetch/FetchSequenceBySwissProtID.java | 63 +
.../bioinf/database/fetch/SequenceRetriever.java | 68 +
src/uk/ac/man/bioinf/debug/AbstractDebug.java | 92 +
src/uk/ac/man/bioinf/debug/Debug.java | 210 +
src/uk/ac/man/bioinf/debug/DebugInterface.java | 79 +
src/uk/ac/man/bioinf/debug/DebugMultiplexer.java | 341 +
src/uk/ac/man/bioinf/debug/DefaultDebug.java | 77 +
src/uk/ac/man/bioinf/debug/DefaultFileDebug.java | 85 +
src/uk/ac/man/bioinf/debug/NullDebug.java | 67 +
src/uk/ac/man/bioinf/gui/color/ColorGenerator.java | 93 +
src/uk/ac/man/bioinf/gui/color/ColorList.java | 126 +
src/uk/ac/man/bioinf/gui/color/ColorMap.java | 87 +
.../ac/man/bioinf/gui/color/ColorMapException.java | 60 +
src/uk/ac/man/bioinf/gui/color/ColorStore.java | 146 +
.../man/bioinf/gui/color/DoubleArrayColorMap.java | 106 +
.../gui/color/IndividualElementColorMap.java | 143 +
.../gui/color/PercentIDVarianceColorMap.java | 145 +
src/uk/ac/man/bioinf/gui/color/SingleColorMap.java | 94 +
.../man/bioinf/gui/color/ThreadableColorMap.java | 64 +
.../ac/man/bioinf/gui/color/ThreadedColorMap.java | 175 +
src/uk/ac/man/bioinf/gui/misc/ChunkyListModel.java | 362 +
.../man/bioinf/gui/misc/SwappingListBasicUI.java | 145 +
.../bioinf/gui/optionable/OptionableJFrame.java | 288 +
.../gui/optionable/OptionableJSplitPane.java | 160 +
.../ac/man/bioinf/gui/util/ApplicationFrame.java | 377 +
.../ac/man/bioinf/gui/util/PopUpHtmlDisplay.java | 61 +
src/uk/ac/man/bioinf/gui/util/SwingWorker.java | 147 +
src/uk/ac/man/bioinf/gui/util/TripletPanel.java | 121 +
.../ac/man/bioinf/gui/util/forms/DecimalField.java | 73 +
.../bioinf/gui/util/forms/FormattedDocument.java | 70 +
.../ac/man/bioinf/gui/util/forms/IntegerField.java | 97 +
.../man/bioinf/gui/util/forms/PasswordDialog.java | 139 +
.../man/bioinf/gui/util/forms/ValidatedForm.java | 414 +
.../bioinf/gui/util/forms/WholeNumberField.java | 82 +
.../bioinf/gui/viewer/AlignmentSelectionModel.java | 151 +
.../gui/viewer/AlignmentSelectionRenderer.java | 63 +
.../gui/viewer/AlignmentViewerCellRenderer.java | 97 +
.../BorderFastAlignmentViewerCellRenderer.java | 103 +
.../bioinf/gui/viewer/ButtonViewerPopupMenu.java | 99 +
.../ColorFastAlignmentViewerCellRenderer.java | 94 +
.../CursorLessFastAlignmentViewerCellRenderer.java | 87 +
.../viewer/DefaultAlignmentSelectionRenderer.java | 71 +
.../viewer/DefaultAlignmentViewerCellRenderer.java | 135 +
.../DefaultFastAlignmentViewerCellRenderer.java | 131 +
.../bioinf/gui/viewer/DefaultSequenceCursor.java | 115 +
.../viewer/FastAlignmentViewerCellRenderer.java | 104 +
src/uk/ac/man/bioinf/gui/viewer/Install.java | 119 +
.../gui/viewer/InvertedScrollPaneLayout.java | 327 +
.../bioinf/gui/viewer/JAlignmentButtonPanel.java | 269 +
.../ac/man/bioinf/gui/viewer/JAlignmentRuler.java | 248 +
.../ac/man/bioinf/gui/viewer/JAlignmentViewer.java | 900 +++
.../man/bioinf/gui/viewer/JChangedScrollPane.java | 83 +
.../man/bioinf/gui/viewer/JLayableScrollPane.java | 89 +
...MultiplexerFastAlignmentViewerCellRenderer.java | 180 +
.../gui/viewer/NullAlignmentSelectionModel.java | 137 +
.../bioinf/gui/viewer/PrintableAlignmentPanel.java | 65 +
.../gui/viewer/PrintableJAlignmentViewer.java | 130 +
.../man/bioinf/gui/viewer/ReadonlyException.java | 96 +
.../ac/man/bioinf/gui/viewer/SequenceCursor.java | 97 +
.../gui/viewer/SingleAlignmentSelectionModel.java | 191 +
.../TextFastAlignmentViewerCellRenderer.java | 103 +
.../gui/viewer/event/AlignmentSelectionEvent.java | 90 +
.../viewer/event/AlignmentSelectionListener.java | 63 +
.../event/AlignmentSelectionListenerSupport.java | 83 +
.../gui/viewer/event/ChangeListenerSupport.java | 86 +
.../bioinf/gui/viewer/plaf/AlignmentRulerUI.java | 62 +
.../bioinf/gui/viewer/plaf/AlignmentViewerUI.java | 90 +
.../gui/viewer/plaf/BasicAlignmentRulerUI.java | 181 +
.../gui/viewer/plaf/BasicAlignmentViewerUI.java | 1061 +++
.../gui/viewer/plaf/MetalAlignmentViewerUI.java | 61 +
.../gui/viewer/test/AlignmentViewerTest.java | 355 +
.../bioinf/gui/viewer/test/BasicWindowMonitor.java | 30 +
.../bioinf/gui/viewer/test/ButtonPanelTest.java | 87 +
.../viewer/test/CellRendererPaneReplacement.java | 115 +
src/uk/ac/man/bioinf/gui/viewer/test/Makefile | 73 +
.../gui/viewer/test/SingleSelectionModelTest.java | 71 +
.../man/bioinf/gui/viewer/test/SliderExample.java | 56 +
src/uk/ac/man/bioinf/io/AlignmentInputParser.java | 109 +
src/uk/ac/man/bioinf/io/AlignmentOutputParser.java | 89 +
.../bioinf/io/DefaultParserExceptionHandler.java | 73 +
.../io/InvalidSequenceTypeParserException.java | 96 +
src/uk/ac/man/bioinf/io/NarrowedInputStream.java | 222 +
.../man/bioinf/io/NullParserExceptionHandler.java | 83 +
src/uk/ac/man/bioinf/io/ParserException.java | 137 +
.../ac/man/bioinf/io/ParserExceptionHandler.java | 71 +
src/uk/ac/man/bioinf/io/SequenceInputParser.java | 66 +
.../ac/man/bioinf/io/SequenceWriterException.java | 62 +
.../ac/man/bioinf/io/UnknownElementException.java | 94 +
.../AbstractProteinAlignmentInputParser.java | 148 +
.../AbstractProteinSequenceInputParser.java | 115 +
.../man/bioinf/io/parsers/FastaSequenceParser.java | 118 +
.../ac/man/bioinf/io/parsers/MotProteinParser.java | 122 +
.../io/parsers/PIRProteinAlignmentParser.java | 299 +
.../man/bioinf/io/test/AlignmentParserIOTest.java | 115 +
.../bioinf/io/test/AlignmentParserInputTest.java | 101 +
.../module/AbstractEnumeratedModuleIdentifier.java | 158 +
.../ac/man/bioinf/module/DefaultModuleContext.java | 74 +
.../module/DefaultModuleFactoryInstance.java | 317 +
.../man/bioinf/module/GenericModuleIdentifier.java | 96 +
src/uk/ac/man/bioinf/module/Module.java | 298 +
src/uk/ac/man/bioinf/module/ModuleContext.java | 156 +
src/uk/ac/man/bioinf/module/ModuleException.java | 104 +
.../ac/man/bioinf/module/ModuleExceptionType.java | 97 +
.../man/bioinf/module/ModuleFactoryInstance.java | 182 +
src/uk/ac/man/bioinf/module/ModuleIdentifier.java | 82 +
.../ac/man/bioinf/module/ModuleIdentifierList.java | 180 +
src/uk/ac/man/bioinf/module/ModuleList.java | 177 +
.../man/bioinf/module/ModuleStorageStructure.java | 197 +
.../ac/man/bioinf/module/NoSuchRequiredModule.java | 69 +
src/uk/ac/man/bioinf/module/NullModuleFactory.java | 150 +
.../bioinf/sequence/AbstractEditableSequence.java | 173 +
.../bioinf/sequence/AbstractMutableSequence.java | 114 +
.../ac/man/bioinf/sequence/AbstractSequence.java | 170 +
.../sequence/ComplexEditableGappedSequence.java | 63 +
.../bioinf/sequence/DefaultEditableSequence.java | 149 +
src/uk/ac/man/bioinf/sequence/DefaultSequence.java | 134 +
.../ac/man/bioinf/sequence/EditableSequence.java | 125 +
src/uk/ac/man/bioinf/sequence/Element.java | 71 +
src/uk/ac/man/bioinf/sequence/EmptySequence.java | 114 +
.../sequence/InvalidSequenceTypeException.java | 64 +
src/uk/ac/man/bioinf/sequence/MutableSequence.java | 69 +
.../sequence/NoSuchSequenceElementException.java | 76 +
src/uk/ac/man/bioinf/sequence/Residue.java | 58 +
src/uk/ac/man/bioinf/sequence/Sequence.java | 127 +
.../ac/man/bioinf/sequence/SequenceException.java | 63 +
src/uk/ac/man/bioinf/sequence/SequenceFactory.java | 169 +
src/uk/ac/man/bioinf/sequence/SequenceType.java | 153 +
src/uk/ac/man/bioinf/sequence/Sequences.java | 339 +
.../sequence/alignment/AbstractGappedSequence.java | 201 +
.../alignment/AbstractSequenceAlignment.java | 471 ++
.../bioinf/sequence/alignment/AlignmentColumn.java | 142 +
.../sequence/alignment/DefaultGappedSequence.java | 394 +
.../alignment/DefaultSequenceAlignment.java | 516 ++
.../sequence/alignment/EmptyGappedSequence.java | 202 +
.../sequence/alignment/EmptySequenceAlignment.java | 234 +
src/uk/ac/man/bioinf/sequence/alignment/Gap.java | 85 +
.../bioinf/sequence/alignment/GappedSequence.java | 148 +
.../alignment/NoGapAtThisPositionException.java | 99 +
.../alignment/NoSuchSequenceException.java | 77 +
.../sequence/alignment/SequenceAlignment.java | 227 +
.../alignment/SingleSequenceAlignment.java | 96 +
.../sequence/alignment/event/AlignmentEvent.java | 130 +
.../alignment/event/AlignmentEventProvider.java | 88 +
.../alignment/event/AlignmentEventType.java | 116 +
.../alignment/event/AlignmentListener.java | 69 +
.../alignment/event/AlignmentListenerSupport.java | 158 +
.../alignment/event/AlignmentVetoException.java | 83 +
.../alignment/event/VetoableAlignmentEvent.java | 72 +
.../alignment/event/VetoableAlignmentListener.java | 76 +
.../sequence/complex/AbstractComplexSequence.java | 178 +
.../complex/AbstractComplexSequenceType.java | 114 +
.../sequence/complex/AbstractModification.java | 79 +
.../bioinf/sequence/complex/ComplexElement.java | 63 +
.../sequence/complex/ComplexElementFactory.java | 125 +
.../complex/ComplexElementFactoryInterface.java | 68 +
.../bioinf/sequence/complex/ComplexSequence.java | 87 +
.../sequence/complex/ComplexSequenceType.java | 97 +
.../sequence/complex/DefaultComplexElement.java | 168 +
.../sequence/complex/DefaultComplexSequence.java | 141 +
.../complex/DefaultComplexSequenceType.java | 143 +
.../complex/DefaultGappedComplexSequence.java | 267 +
.../sequence/complex/GappedComplexSequence.java | 59 +
.../sequence/complex/GenericModification.java | 82 +
.../complex/HardComplexElementFactory.java | 144 +
.../complex/HardModificationSetFactory.java | 131 +
.../IllegalDuplicateModificationException.java | 62 +
.../man/bioinf/sequence/complex/Methylation.java | 68 +
.../man/bioinf/sequence/complex/Modification.java | 63 +
.../sequence/complex/ModificationFactory.java | 105 +
.../bioinf/sequence/complex/ModificationSet.java | 143 +
.../sequence/complex/ModificationSetFactory.java | 89 +
.../complex/ModificationSetFactoryInterface.java | 68 +
.../complex/NoSuchModificationException.java | 61 +
.../sequence/complex/SingletonModification.java | 69 +
.../complex/WeakComplexElementFactory.java | 188 +
.../complex/WeakModificationSetFactory.java | 136 +
src/uk/ac/man/bioinf/sequence/complex/package.html | 13 +
.../man/bioinf/sequence/event/SequenceEvent.java | 132 +
.../sequence/event/SequenceEventProvider.java | 90 +
.../bioinf/sequence/event/SequenceEventType.java | 82 +
.../bioinf/sequence/event/SequenceListener.java | 66 +
.../sequence/event/SequenceListenerSupport.java | 183 +
.../sequence/event/SequenceVetoException.java | 85 +
.../sequence/event/VetoableSequenceEvent.java | 72 +
.../sequence/event/VetoableSequenceListener.java | 73 +
.../sequence/geom/SequenceAlignmentDimension.java | 169 +
.../sequence/geom/SequenceAlignmentPoint.java | 250 +
.../sequence/geom/SequenceAlignmentRectangle.java | 379 +
.../sequence/geom/SequenceAlignmentShape.java | 64 +
.../group/AbstractGappedSequenceGroup.java | 78 +
.../sequence/group/DefaultGappedSequenceGroup.java | 137 +
.../bioinf/sequence/group/GappedSequenceGroup.java | 67 +
.../sequence/group/GroupSequenceAlignment.java | 406 +
.../man/bioinf/sequence/group/SequenceGroup.java | 115 +
.../sequence/identifier/AbstractIdentifier.java | 80 +
.../sequence/identifier/DatabaseIdentifier.java | 82 +
.../man/bioinf/sequence/identifier/FileSource.java | 75 +
.../bioinf/sequence/identifier/Identifiable.java | 63 +
.../man/bioinf/sequence/identifier/Identifier.java | 81 +
.../identifier/MalformedAccessionException.java | 64 +
.../bioinf/sequence/identifier/NoIdentifier.java | 92 +
.../man/bioinf/sequence/identifier/NoSource.java | 67 +
.../bioinf/sequence/identifier/ReaderSource.java | 69 +
.../bioinf/sequence/identifier/SequenceSource.java | 68 +
.../sequence/identifier/SimpleIdentifier.java | 81 +
.../bioinf/sequence/identifier/SimpleSource.java | 70 +
.../ac/man/bioinf/sequence/identifier/Source.java | 73 +
.../sequence/identifier/StreamSequenceSource.java | 76 +
.../sequence/identifier/SwissProtIdentifier.java | 81 +
.../sequence/identifier/URLSequenceSource.java | 78 +
src/uk/ac/man/bioinf/sequence/package.html | 12 +
.../test/ComplexElementAndModificationTest.java | 256 +
.../bioinf/sequence/test/ComplexSequenceTest.java | 187 +
.../bioinf/sequence/test/EditableSequenceTest.java | 241 +
.../bioinf/sequence/test/GappableSequenceTest.java | 215 +
.../bioinf/sequence/test/GappedSequenceTest.java | 134 +
.../sequence/test/SequenceAlignmentTest.java | 246 +
.../bioinf/sequence/test/SequenceColumnTest.java | 79 +
.../bioinf/sequence/test/SequenceFactoryTest.java | 85 +
.../ac/man/bioinf/sequence/test/SequencesTest.java | 104 +
.../man/bioinf/sequence/types/AbstractElement.java | 102 +
.../types/AbstractEnumeratedSequenceType.java | 85 +
.../sequence/types/AbstractSequenceType.java | 168 +
src/uk/ac/man/bioinf/sequence/types/AminoAcid.java | 168 +
.../man/bioinf/sequence/types/DNANucleotide.java | 95 +
.../ac/man/bioinf/sequence/types/DNAResidue.java | 65 +
.../man/bioinf/sequence/types/DNASequenceType.java | 73 +
.../bioinf/sequence/types/EmptySequenceType.java | 115 +
.../bioinf/sequence/types/NucleotideResidue.java | 66 +
.../man/bioinf/sequence/types/ProteinResidue.java | 73 +
.../bioinf/sequence/types/ProteinSequenceType.java | 78 +
.../man/bioinf/sequence/types/RNANucleotide.java | 105 +
.../ac/man/bioinf/sequence/types/RNAResidue.java | 62 +
.../man/bioinf/sequence/types/RNASequenceType.java | 71 +
src/uk/ac/man/bioinf/util/AbstractEnumeration.java | 286 +
src/uk/ac/man/bioinf/util/ArrayManipulation.java | 106 +
src/uk/ac/man/bioinf/util/Changeable.java | 60 +
src/uk/ac/man/bioinf/util/ChangeableEvent.java | 62 +
src/uk/ac/man/bioinf/util/ChangeableListener.java | 59 +
.../man/bioinf/util/ChangeableListenerSupport.java | 84 +
src/uk/ac/man/bioinf/util/CollectionPrinter.java | 86 +
src/uk/ac/man/bioinf/util/Direction.java | 68 +
src/uk/ac/man/bioinf/util/ExceptionHandler.java | 65 +
src/uk/ac/man/bioinf/util/IntArrayList.java | 347 +
.../ac/man/bioinf/util/PackageResourceAdapter.java | 55 +
src/uk/ac/man/bioinf/util/ResourceAdapter.java | 113 +
.../util/SequenceAlignmentToChangeableAdaptor.java | 93 +
1458 files changed, 238371 insertions(+), 422 deletions(-)
diff --git a/README b/README
new file mode 100644
index 0000000..b690743
--- /dev/null
+++ b/README
@@ -0,0 +1,10 @@
+This is the README file for the bioinf packages.
+
+
+These packages are a series of libraries and applications written to
+allow the analysis and visualisation of various biological data.
+
+
+For further information please see the doc/ subdirectory.
+
+
diff --git a/bin/cinema b/bin/cinema
new file mode 100755
index 0000000..85ea182
--- /dev/null
+++ b/bin/cinema
@@ -0,0 +1,84 @@
+#!/bin/sh
+
+###
+### Launch script for Cinema.
+###
+### Copyright (c) 2001 Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+
+###
+### This is the definative launch script for Cinema. I have scripts in
+### other languages also, but if they differ in their functionality,
+### all the others are wrong and this one is right.
+###
+
+## I wanted to do some command line parsing here, but my shell
+## scripting is not really up to it, which is a pity. The end solution
+## to this is probably to do as much of the command liner parsing in
+## Java as possible.
+
+
+## This is the location of the main install directory where Cinema
+## should find all most of its jar files.
+CINEMA_LIB=../lib
+
+## This is the location of any user extensions.
+USER_EXTENSIONS=~/.cinema/ext
+
+VERBOSE=0
+
+# while getopts :L:U:D:V c
+
+# do
+# case $c in
+# L) CINEMA_LIB=$OPTARG;;
+# U) USER_EXTENSIONS=$OPTARG;;
+# V) VERBOSE=1;;
+# ## we want to be able to pass -D options as java virtual
+# ## machine options. This duplicates them so that we can pass
+# ## them before the java class argument. There presence after
+# ## the class as well should not cause any problems and I don't
+# ## know a quick way of removing them.
+# D) JVM_OPTIONS="${JVM_OPTIONS} -D$OPTARG";;
+# ## pass everything else onwards
+# \?) echo parsing unknown $OPTARG $c
+# OTHER_OPTIONS="${OTHER_OPTIONS} -$OPTARG";;
+# esac
+# done
+
+
+## identify the user jars and generate the relevent string
+for jar_file in ${USER_EXTENSIONS}/*.jar
+do
+ user_jars=${user_jars}:$jar_file
+done
+## also let the users have files not in jars
+user_jars=${user_jars}:${USER_EXTENSIONS}
+
+## and the same for cinema jars
+for jar_file in ${CINEMA_LIB}/*.jar
+do
+ cinema_jars=${cinema_jars}:$jar_file
+done
+
+## and finally for any external libraries
+for jar_file in ${CINEMA_LIB}/ext/*.jar
+do
+ ext_jars=${ext_jars}:$jar_file
+done
+
+# classpath
+classpath=${user_jars}${cinema_jars}${ext_jars}
+
+
+##
+## run CINEMA
+##
+COMMAND_LINE="java -classpath ${classpath} ${JVM_OPTIONS} uk.ac.man.bioinf.apps.cinema.Cinema ${OTHER_ARGUMENTS} $*"
+
+## print out the command line if verbose
+if test $VERBOSE -eq 1
+ then
+ echo "Running Cinema as ${COMMAND_LINE}"
+fi
+
+java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS $*
diff --git a/bin/cinema.cygwin b/bin/cinema.cygwin
new file mode 100755
index 0000000..4f87c3c
--- /dev/null
+++ b/bin/cinema.cygwin
@@ -0,0 +1,81 @@
+#!/bin/sh
+
+###
+### Launch script for Cinema.
+###
+### Copyright (c) 2001 Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+
+###
+### This is the definative launch script for Cinema. I have scripts in
+### other languages also, but if they differ in their functionality,
+### all the others are wrong and this one is right.
+###
+
+## Parse the command line. We do not actually want to parse the entire
+## command as most of the work should be done by cinema. Unfortunately
+## some options have to be set before the JVM is launched so we have
+## to do some work here.
+
+
+## This is the location of the main install directory where Cinema
+## should find all most of its jar files.
+CINEMA_LIB=../lib
+
+## This is the location of any user extensions.
+USER_EXTENSIONS=~/.cinema/ext
+
+VERBOSE=1
+
+# while getopts L:U:D:V c
+
+# do
+# case $c in
+# L) CINEMA_LIB=$OPTARG;;
+# U) USER_EXTENSIONS=$OPTARG;;
+# V) VERBOSE=1;;
+# ## we want to be able to pass -D options as java virtual
+# ## machine options. This duplicates them so that we can pass
+# ## them before the java class argument. There presence after
+# ## the class as well should not cause any problems and I don't
+# ## know a quick way of removing them.
+# D) JVM_OPTIONS="${JVM_OPTIONS} -D$OPTARG";;
+# ## pass everything else onwards
+# \?) OTHER_OPTIONS="${OTHER_OPTIONS}-${c}$OPTARG";;
+# esac
+# done
+
+## identify the user jars and generate the relevent string
+for jar_file in ${USER_EXTENSIONS}/*.jar
+do
+ user_jars=${user_jars}";"$jar_file
+done
+
+## and the same for cinema jars
+for jar_file in ${CINEMA_LIB}/*.jar
+do
+ cinema_jars=${cinema_jars}";"$jar_file
+done
+
+
+## and finally for any external libraries
+for jar_file in ${CINEMA_LIB}/ext/*.jar
+do
+ ext_jars=${ext_jars}";"$jar_file
+done
+
+# classpath
+classpath=${user_jars}${cinema_jars}${ext_jars}
+
+
+##
+## run CINEMA
+##
+COMMAND_LINE="java -classpath ${classpath} ${JVM_OPTIONS} uk.ac.man.bioinf.apps.cinema.Cinema ${OTHER_ARGUMENTS}"
+
+## print out the command line if verbose
+if test $VERBOSE -eq 1
+ then
+ echo "Running Cinema as ${COMMAND_LINE}"
+fi
+
+java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS
diff --git a/bin/cinema.pl b/bin/cinema.pl
new file mode 100755
index 0000000..0f5f991
--- /dev/null
+++ b/bin/cinema.pl
@@ -0,0 +1,78 @@
+#!/usr/bin/perl
+
+
+### This is a launch script for Cinema
+
+
+###
+### This is a direct port of the Cinema sh script which is to be
+### considered the definative version in terms of functionality.
+###
+### This is particularly true in the case of this script as I am a
+### registered member of the perl post-traumatic stress disorder
+### self-help society.
+###
+### Copyright (c) 2001 Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+###
+
+
+
+use Getopt::Std;
+
+my $CINEMA_LIB="../lib";
+my $USER_EXTENSIONS="~/.cinema/ext";
+my $VERBOSE=0;
+my $JVM_OPTIONS;
+
+getopts( 'L:U:D:V' );
+
+
+if( $opt_L ){
+ $CINEMA_LIB = $opt_L;
+}
+
+if( $opt_U ){
+ $USER_EXTENSIONS=$opt_U;
+}
+
+if( $opt_V ){
+ $VERBOSE=$opt_V;
+}
+
+if( $opt_D ){
+ ## I don't think that this will work correctly. Its only going to
+ ## set an single -D option which is a bit of a pain.
+ $JVM_OPTIONS="$JVM_OPTIONS -D$opt_D";
+}
+
+my $jarfile;
+my $user_jars = "";
+my $cinema_jars= "";
+my $ext_jars = "";
+
+
+foreach $jarfile ( glob( "$USER_EXTENSIONS/*jar" ) ){
+ $user_jars.=":$jarfile";
+}
+
+foreach $jarfile ( glob( "$CINEMA_LIB/*jar" ) ){
+ $cinema_jars.=":$jarfile";
+}
+
+foreach $jarfile ( glob( "$CINEMA_LIB/ext/*jar" ) ){
+ $ext_jars.=":$jarfile";
+}
+
+my $classpath="$user_jars$cinema_jars$ext_jars";
+
+if( $VERBOSE ){
+ print "java -classpath $classpath $JVM_OPTIONS uk.ac.man.bioinf.apps.cinema.Cinema @ARGV";
+}
+
+print `java -classpath $classpath $JVM_OPTIONS uk.ac.man.bioinf.apps.cinema.Cinema @ARGV`;
+
+
+
+
+
+
diff --git a/classes/uk/ac/man/bioinf/Y.class b/classes/uk/ac/man/bioinf/Y.class
new file mode 100644
index 0000000..75e3c3a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/Y.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.class b/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.class
new file mode 100644
index 0000000..5d967a9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.class b/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.class
new file mode 100644
index 0000000..3eaba3f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.class b/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.class
new file mode 100644
index 0000000..3c3cab2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence$1.class b/classes/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence$1.class
new file mode 100644
index 0000000..40f4620
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence$1.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.class b/classes/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.class
new file mode 100644
index 0000000..f269189
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.class b/classes/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.class
new file mode 100644
index 0000000..261bd10
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence$1.class b/classes/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence$1.class
new file mode 100644
index 0000000..c7cc949
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence$1.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.class b/classes/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.class
new file mode 100644
index 0000000..8c27379
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.class b/classes/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.class
new file mode 100644
index 0000000..754b774
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.class b/classes/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.class
new file mode 100644
index 0000000..c320479
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.class b/classes/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.class
new file mode 100644
index 0000000..d5e3f5e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.class differ
diff --git a/classes/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.class b/classes/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.class
new file mode 100644
index 0000000..bb4bc82
Binary files /dev/null and b/classes/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/Cinema.class b/classes/uk/ac/man/bioinf/apps/cinema/Cinema.class
new file mode 100644
index 0000000..6ed7d7d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/Cinema.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaBoot.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaBoot.class
new file mode 100644
index 0000000..981c4eb
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaBoot.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.class
new file mode 100644
index 0000000..c4f53da
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.class
new file mode 100644
index 0000000..f207b6f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaModule.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaModule.class
new file mode 100644
index 0000000..96920d7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.class
new file mode 100644
index 0000000..96bf6a2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaProperties.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaProperties.class
new file mode 100644
index 0000000..30f8a9b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaProperties.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaShared.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaShared.class
new file mode 100644
index 0000000..362125d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaShared.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory$1.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory$1.class
new file mode 100644
index 0000000..9e5b624
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.class b/classes/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.class
new file mode 100644
index 0000000..7da7ced
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.class
new file mode 100644
index 0000000..2b6ecc9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.class b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.class
new file mode 100644
index 0000000..8eebbcd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.class
new file mode 100644
index 0000000..e6030db
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector$ClosureAbstractAction.class b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector$ClosureAbstractAction.class
new file mode 100644
index 0000000..c8bc980
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector$ClosureAbstractAction.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.class b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.class
new file mode 100644
index 0000000..5361f2d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.class
new file mode 100644
index 0000000..5d9d9a5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.class
new file mode 100644
index 0000000..feff6e6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.class
new file mode 100644
index 0000000..1e3cf8f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.class b/classes/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.class
new file mode 100644
index 0000000..db63f9a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.class
new file mode 100644
index 0000000..a381a78
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.class
new file mode 100644
index 0000000..ae1c238
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.class
new file mode 100644
index 0000000..df73630
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.class
new file mode 100644
index 0000000..33f425f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.class
new file mode 100644
index 0000000..59ec902
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.class
new file mode 100644
index 0000000..f697a4c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData$1.class b/classes/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData$1.class
new file mode 100644
index 0000000..9e49074
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.class
new file mode 100644
index 0000000..9277df5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.class
new file mode 100644
index 0000000..27dcb2e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.class
new file mode 100644
index 0000000..27da586
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.class
new file mode 100644
index 0000000..8b113ca
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.class
new file mode 100644
index 0000000..e0977c8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.class
new file mode 100644
index 0000000..a50314e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.class
new file mode 100644
index 0000000..4576c07
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay$ClosureAbstractAction.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay$ClosureAbstractAction.class
new file mode 100644
index 0000000..f9815e4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay$ClosureAbstractAction.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.class
new file mode 100644
index 0000000..109875a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.class
new file mode 100644
index 0000000..9b5925d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.class
new file mode 100644
index 0000000..9d9f38c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.class b/classes/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.class
new file mode 100644
index 0000000..426fccd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.class b/classes/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.class
new file mode 100644
index 0000000..b8e9f6b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.class b/classes/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.class
new file mode 100644
index 0000000..bace29a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.class
new file mode 100644
index 0000000..dd5fbf9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui$1.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui$1.class
new file mode 100644
index 0000000..7fee4f4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui$2.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui$2.class
new file mode 100644
index 0000000..fe0e9da
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.class
new file mode 100644
index 0000000..871a5b3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.class
new file mode 100644
index 0000000..dc3183d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView$1.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView$1.class
new file mode 100644
index 0000000..d2d7fab
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.class
new file mode 100644
index 0000000..3fe9d01
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.class
new file mode 100644
index 0000000..37acf16
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.class
new file mode 100644
index 0000000..479b252
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.class
new file mode 100644
index 0000000..eed537d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.class
new file mode 100644
index 0000000..e9bdd5a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.class
new file mode 100644
index 0000000..fcb0edf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.class b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.class
new file mode 100644
index 0000000..0fdd4f6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.class b/classes/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.class
new file mode 100644
index 0000000..ef06edf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager$AnchorListener.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager$AnchorListener.class
new file mode 100644
index 0000000..d940c84
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager$AnchorListener.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.class
new file mode 100644
index 0000000..b7ed434
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup$CinemaGroupAlignmentIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup$CinemaGroupAlignmentIdentifier.class
new file mode 100644
index 0000000..28770dc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup$CinemaGroupAlignmentIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.class
new file mode 100644
index 0000000..d6f850e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$GroupListCellRenderer.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$GroupListCellRenderer.class
new file mode 100644
index 0000000..47133d8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$GroupListCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$GroupMemberCellRenderer.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$GroupMemberCellRenderer.class
new file mode 100644
index 0000000..090042f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$GroupMemberCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$InformativeSwappingListBasicUI$InformativeSwappingListHandler.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$InformativeSwappingListBasicUI$InformativeSwappingListHandler.class
new file mode 100644
index 0000000..8937c89
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$InformativeSwappingListBasicUI$InformativeSwappingListHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$InformativeSwappingListBasicUI.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$InformativeSwappingListBasicUI.class
new file mode 100644
index 0000000..d38dfa8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame$InformativeSwappingListBasicUI.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.class
new file mode 100644
index 0000000..9c65ed5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.class
new file mode 100644
index 0000000..123c797
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.class
new file mode 100644
index 0000000..74b80f2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$1.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$1.class
new file mode 100644
index 0000000..5c5be02
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$AddToGroup.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$AddToGroup.class
new file mode 100644
index 0000000..51f3934
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$AddToGroup.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$DeleteGroupActionListener.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$DeleteGroupActionListener.class
new file mode 100644
index 0000000..dc270d4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule$DeleteGroupActionListener.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.class b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.class
new file mode 100644
index 0000000..afd2a9f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput$1.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput$1.class
new file mode 100644
index 0000000..099521e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.class
new file mode 100644
index 0000000..4a7fe1e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.class
new file mode 100644
index 0000000..c1a21c5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput$1.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput$1.class
new file mode 100644
index 0000000..2db154b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput$2.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput$2.class
new file mode 100644
index 0000000..e2a2c15
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.class
new file mode 100644
index 0000000..3a390a7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.class b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.class
new file mode 100644
index 0000000..76932c9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.class b/classes/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.class
new file mode 100644
index 0000000..2e2ccc6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.class
new file mode 100644
index 0000000..d7b14f4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.class b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.class
new file mode 100644
index 0000000..eb0e1a7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.class b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.class
new file mode 100644
index 0000000..2a6a6d7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.class b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.class
new file mode 100644
index 0000000..c027217
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.class b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.class
new file mode 100644
index 0000000..a6e6705
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.class
new file mode 100644
index 0000000..6fcdfa1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.class
new file mode 100644
index 0000000..b591e1e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame$MotifFormatFileChooser.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame$MotifFormatFileChooser.class
new file mode 100644
index 0000000..d2cbad8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame$MotifFormatFileChooser.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.class
new file mode 100644
index 0000000..7775e59
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.class
new file mode 100644
index 0000000..3270a97
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule$1.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule$1.class
new file mode 100644
index 0000000..02de51c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.class
new file mode 100644
index 0000000..266033d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$1.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$1.class
new file mode 100644
index 0000000..f04b12b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$2.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$2.class
new file mode 100644
index 0000000..a8d51ba
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$SelectionInfo.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$SelectionInfo.class
new file mode 100644
index 0000000..d6942be
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel$SelectionInfo.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.class b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.class
new file mode 100644
index 0000000..23d78b8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.class b/classes/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.class
new file mode 100644
index 0000000..6aff025
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$1.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$1.class
new file mode 100644
index 0000000..49d643b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$2.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$2.class
new file mode 100644
index 0000000..1836b0e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$DebugImpl.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$DebugImpl.class
new file mode 100644
index 0000000..7c9c5b9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug$DebugImpl.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.class
new file mode 100644
index 0000000..8e48fe8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.class
new file mode 100644
index 0000000..05bd694
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$1.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$1.class
new file mode 100644
index 0000000..60d3da8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$2.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$2.class
new file mode 100644
index 0000000..d89dacd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$QuitExitManager.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$QuitExitManager.class
new file mode 100644
index 0000000..504ad1b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit$QuitExitManager.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.class
new file mode 100644
index 0000000..d7a7d18
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.class b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.class
new file mode 100644
index 0000000..8ef2d26
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.class
new file mode 100644
index 0000000..0ecbcdf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$1.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$1.class
new file mode 100644
index 0000000..a0f4b40
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$2.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$2.class
new file mode 100644
index 0000000..87422a5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$DebugImpl.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$DebugImpl.class
new file mode 100644
index 0000000..2703e62
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug$DebugImpl.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.class
new file mode 100644
index 0000000..fa0bc55
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.class
new file mode 100644
index 0000000..48d9830
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.class
new file mode 100644
index 0000000..faf839e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.class
new file mode 100644
index 0000000..e991b6c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.class
new file mode 100644
index 0000000..be057c9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.class
new file mode 100644
index 0000000..df8596b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.class
new file mode 100644
index 0000000..0e6a97e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp$1.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp$1.class
new file mode 100644
index 0000000..f44f0fc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp$FramedAbstractAction.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp$FramedAbstractAction.class
new file mode 100644
index 0000000..1e5af3b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp$FramedAbstractAction.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.class
new file mode 100644
index 0000000..b60a352
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements$FramedAbstractAction.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements$FramedAbstractAction.class
new file mode 100644
index 0000000..afb89e1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements$FramedAbstractAction.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements$ResizerGui.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements$ResizerGui.class
new file mode 100644
index 0000000..7340997
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements$ResizerGui.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.class
new file mode 100644
index 0000000..b752acb
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.class
new file mode 100644
index 0000000..6a3ee80
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation$1.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation$1.class
new file mode 100644
index 0000000..de52694
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation$2.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation$2.class
new file mode 100644
index 0000000..ae4df35
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation$2.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.class
new file mode 100644
index 0000000..3c7a19f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.class
new file mode 100644
index 0000000..b9794fa
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.class b/classes/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.class
new file mode 100644
index 0000000..9e64fe1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID$1.class b/classes/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID$1.class
new file mode 100644
index 0000000..60ad98c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.class b/classes/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.class
new file mode 100644
index 0000000..3541cc5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints$1.class b/classes/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints$1.class
new file mode 100644
index 0000000..56ecb20
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.class b/classes/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.class
new file mode 100644
index 0000000..9f48527
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch$1.class b/classes/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch$1.class
new file mode 100644
index 0000000..4a21ea6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.class b/classes/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.class
new file mode 100644
index 0000000..094fd94
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/SequenceSearch$1.class b/classes/uk/ac/man/bioinf/apps/commandline/SequenceSearch$1.class
new file mode 100644
index 0000000..216f3ec
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/SequenceSearch$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/commandline/SequenceSearch.class b/classes/uk/ac/man/bioinf/apps/commandline/SequenceSearch.class
new file mode 100644
index 0000000..5ca7cf5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/commandline/SequenceSearch.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/AnonInvoker.class b/classes/uk/ac/man/bioinf/apps/invoker/AnonInvoker.class
new file mode 100644
index 0000000..47b5265
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/AnonInvoker.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/Invoker.class b/classes/uk/ac/man/bioinf/apps/invoker/Invoker.class
new file mode 100644
index 0000000..02debe6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/Invoker.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.class b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.class
new file mode 100644
index 0000000..4adcb1a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue$1.class b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue$1.class
new file mode 100644
index 0000000..c8901ba
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.class b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.class
new file mode 100644
index 0000000..3fb0c40
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.class b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.class
new file mode 100644
index 0000000..ef71b90
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.class b/classes/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.class
new file mode 100644
index 0000000..674ce9d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.class b/classes/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.class
new file mode 100644
index 0000000..9ce529e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.class b/classes/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.class
new file mode 100644
index 0000000..b089127
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/OptionHandler.class b/classes/uk/ac/man/bioinf/apps/optionable/OptionHandler.class
new file mode 100644
index 0000000..193a34c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/OptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/Optionable.class b/classes/uk/ac/man/bioinf/apps/optionable/Optionable.class
new file mode 100644
index 0000000..8cc08e0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/Optionable.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.class b/classes/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.class
new file mode 100644
index 0000000..7a58775
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.class b/classes/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.class
new file mode 100644
index 0000000..c33d928
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/OptionableStateException.class b/classes/uk/ac/man/bioinf/apps/optionable/OptionableStateException.class
new file mode 100644
index 0000000..c736af1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/OptionableStateException.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/optionable/SaveableOptions.class b/classes/uk/ac/man/bioinf/apps/optionable/SaveableOptions.class
new file mode 100644
index 0000000..1f16c40
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/optionable/SaveableOptions.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemEvent.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEvent.class
new file mode 100644
index 0000000..9b9d07f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.class
new file mode 100644
index 0000000..b963ddb
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.class
new file mode 100644
index 0000000..7fa976a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport$ListenerToComparable.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport$ListenerToComparable.class
new file mode 100644
index 0000000..3b5d5a9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport$ListenerToComparable.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.class
new file mode 100644
index 0000000..8caba29
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemListener.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemListener.class
new file mode 100644
index 0000000..c2f92e5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemListener.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.class b/classes/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.class
new file mode 100644
index 0000000..1f5d004
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/ConfigNode.class b/classes/uk/ac/man/bioinf/apps/xml/ConfigNode.class
new file mode 100644
index 0000000..16a249b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/ConfigNode.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/DefaultXMLParser$1.class b/classes/uk/ac/man/bioinf/apps/xml/DefaultXMLParser$1.class
new file mode 100644
index 0000000..2efbc64
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/DefaultXMLParser$1.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.class b/classes/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.class
new file mode 100644
index 0000000..6b1fb0d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.class b/classes/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.class
new file mode 100644
index 0000000..2fb490c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/XMLBootModule$MiniStack.class b/classes/uk/ac/man/bioinf/apps/xml/XMLBootModule$MiniStack.class
new file mode 100644
index 0000000..05aab2a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/XMLBootModule$MiniStack.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/XMLBootModule.class b/classes/uk/ac/man/bioinf/apps/xml/XMLBootModule.class
new file mode 100644
index 0000000..c08259f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/XMLBootModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.class b/classes/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.class
new file mode 100644
index 0000000..062dd99
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/XMLModule.class b/classes/uk/ac/man/bioinf/apps/xml/XMLModule.class
new file mode 100644
index 0000000..b907457
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/XMLModule.class differ
diff --git a/classes/uk/ac/man/bioinf/apps/xml/XMLParserFactory.class b/classes/uk/ac/man/bioinf/apps/xml/XMLParserFactory.class
new file mode 100644
index 0000000..94b0f01
Binary files /dev/null and b/classes/uk/ac/man/bioinf/apps/xml/XMLParserFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.class b/classes/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.class
new file mode 100644
index 0000000..7991f48
Binary files /dev/null and b/classes/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.class differ
diff --git a/classes/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.class b/classes/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.class
new file mode 100644
index 0000000..d527d22
Binary files /dev/null and b/classes/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.class differ
diff --git a/classes/uk/ac/man/bioinf/database/fetch/SequenceRetriever.class b/classes/uk/ac/man/bioinf/database/fetch/SequenceRetriever.class
new file mode 100644
index 0000000..0ba1e7b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/database/fetch/SequenceRetriever.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/AbstractDebug.class b/classes/uk/ac/man/bioinf/debug/AbstractDebug.class
new file mode 100644
index 0000000..b7cf937
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/AbstractDebug.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/Debug.class b/classes/uk/ac/man/bioinf/debug/Debug.class
new file mode 100644
index 0000000..03438a8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/Debug.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/DebugInterface.class b/classes/uk/ac/man/bioinf/debug/DebugInterface.class
new file mode 100644
index 0000000..410d04e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/DebugInterface.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/DebugMultiplexer.class b/classes/uk/ac/man/bioinf/debug/DebugMultiplexer.class
new file mode 100644
index 0000000..73e915c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/DebugMultiplexer.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/DefaultDebug.class b/classes/uk/ac/man/bioinf/debug/DefaultDebug.class
new file mode 100644
index 0000000..1e490b5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/DefaultDebug.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/DefaultFileDebug.class b/classes/uk/ac/man/bioinf/debug/DefaultFileDebug.class
new file mode 100644
index 0000000..3b210a2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/DefaultFileDebug.class differ
diff --git a/classes/uk/ac/man/bioinf/debug/NullDebug.class b/classes/uk/ac/man/bioinf/debug/NullDebug.class
new file mode 100644
index 0000000..39eb651
Binary files /dev/null and b/classes/uk/ac/man/bioinf/debug/NullDebug.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ColorGenerator.class b/classes/uk/ac/man/bioinf/gui/color/ColorGenerator.class
new file mode 100644
index 0000000..9ea0d7e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ColorGenerator.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ColorList.class b/classes/uk/ac/man/bioinf/gui/color/ColorList.class
new file mode 100644
index 0000000..7ce486a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ColorList.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ColorMap.class b/classes/uk/ac/man/bioinf/gui/color/ColorMap.class
new file mode 100644
index 0000000..11f154e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ColorMapException.class b/classes/uk/ac/man/bioinf/gui/color/ColorMapException.class
new file mode 100644
index 0000000..3b84024
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ColorMapException.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ColorStore.class b/classes/uk/ac/man/bioinf/gui/color/ColorStore.class
new file mode 100644
index 0000000..65bd116
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ColorStore.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.class b/classes/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.class
new file mode 100644
index 0000000..9d1959b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.class b/classes/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.class
new file mode 100644
index 0000000..da49770
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.class b/classes/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.class
new file mode 100644
index 0000000..5347a63
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/SingleColorMap.class b/classes/uk/ac/man/bioinf/gui/color/SingleColorMap.class
new file mode 100644
index 0000000..e6194c8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/SingleColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ThreadableColorMap.class b/classes/uk/ac/man/bioinf/gui/color/ThreadableColorMap.class
new file mode 100644
index 0000000..3aa5862
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ThreadableColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ThreadedColorMap$1.class b/classes/uk/ac/man/bioinf/gui/color/ThreadedColorMap$1.class
new file mode 100644
index 0000000..d56b4cf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ThreadedColorMap$1.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/color/ThreadedColorMap.class b/classes/uk/ac/man/bioinf/gui/color/ThreadedColorMap.class
new file mode 100644
index 0000000..4adbce4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/color/ThreadedColorMap.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/misc/ChunkyListModel.class b/classes/uk/ac/man/bioinf/gui/misc/ChunkyListModel.class
new file mode 100644
index 0000000..11af504
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/misc/ChunkyListModel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI$SwappingMouseInputHandler.class b/classes/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI$SwappingMouseInputHandler.class
new file mode 100644
index 0000000..3821a67
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI$SwappingMouseInputHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.class b/classes/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.class
new file mode 100644
index 0000000..c12c3a7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.class b/classes/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.class
new file mode 100644
index 0000000..267a220
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.class b/classes/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.class
new file mode 100644
index 0000000..d155ece
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/ApplicationFrame$1.class b/classes/uk/ac/man/bioinf/gui/util/ApplicationFrame$1.class
new file mode 100644
index 0000000..e9cf0b7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/ApplicationFrame$1.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/ApplicationFrame.class b/classes/uk/ac/man/bioinf/gui/util/ApplicationFrame.class
new file mode 100644
index 0000000..cf9841e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/ApplicationFrame.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.class b/classes/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.class
new file mode 100644
index 0000000..dd17efe
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/TripletPanel.class b/classes/uk/ac/man/bioinf/gui/util/TripletPanel.class
new file mode 100644
index 0000000..021a7b6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/TripletPanel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/DecimalField.class b/classes/uk/ac/man/bioinf/gui/util/forms/DecimalField.class
new file mode 100644
index 0000000..0e63e2d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/DecimalField.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.class b/classes/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.class
new file mode 100644
index 0000000..7ae9e8d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/IntegerField$IntegerDocument.class b/classes/uk/ac/man/bioinf/gui/util/forms/IntegerField$IntegerDocument.class
new file mode 100644
index 0000000..a260b86
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/IntegerField$IntegerDocument.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/IntegerField.class b/classes/uk/ac/man/bioinf/gui/util/forms/IntegerField.class
new file mode 100644
index 0000000..2152372
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/IntegerField.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.class b/classes/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.class
new file mode 100644
index 0000000..1bf018e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm$ModifierCombo.class b/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm$ModifierCombo.class
new file mode 100644
index 0000000..f42de3f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm$ModifierCombo.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm$MyDocumentListener.class b/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm$MyDocumentListener.class
new file mode 100644
index 0000000..1558570
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm$MyDocumentListener.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.class b/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.class
new file mode 100644
index 0000000..9e25938
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/WholeNumberField$WholeNumberDocument.class b/classes/uk/ac/man/bioinf/gui/util/forms/WholeNumberField$WholeNumberDocument.class
new file mode 100644
index 0000000..ee016ae
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/WholeNumberField$WholeNumberDocument.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.class b/classes/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.class
new file mode 100644
index 0000000..afb2236
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.class b/classes/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.class
new file mode 100644
index 0000000..b36e4ea
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.class
new file mode 100644
index 0000000..418f5d0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..225794c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..a56dd62
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.class b/classes/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.class
new file mode 100644
index 0000000..bdd86bd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..f231eb6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..20d6e65
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.class
new file mode 100644
index 0000000..d735b3c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..aa3f280
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..3fe2fd0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.class b/classes/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.class
new file mode 100644
index 0000000..129f026
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..162b3ca
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/Install.class b/classes/uk/ac/man/bioinf/gui/viewer/Install.class
new file mode 100644
index 0000000..ce7b649
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/Install.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.class b/classes/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.class
new file mode 100644
index 0000000..bc0db75
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel$SequenceButtonListener.class b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel$SequenceButtonListener.class
new file mode 100644
index 0000000..cbedda0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel$SequenceButtonListener.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.class b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.class
new file mode 100644
index 0000000..9fa9c18
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler$SequenceAlignmentBoundRangeModelBridge.class b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler$SequenceAlignmentBoundRangeModelBridge.class
new file mode 100644
index 0000000..b1a3616
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler$SequenceAlignmentBoundRangeModelBridge.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.class b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.class
new file mode 100644
index 0000000..e5aa814
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.class b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.class
new file mode 100644
index 0000000..b1a3bc5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.class b/classes/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.class
new file mode 100644
index 0000000..476feb4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.class b/classes/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.class
new file mode 100644
index 0000000..eb1e93b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..2f9c313
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.class b/classes/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.class
new file mode 100644
index 0000000..d54a5a5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.class b/classes/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.class
new file mode 100644
index 0000000..a6eaf41
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.class b/classes/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.class
new file mode 100644
index 0000000..c507eaf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/ReadonlyException.class b/classes/uk/ac/man/bioinf/gui/viewer/ReadonlyException.class
new file mode 100644
index 0000000..27f74f4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/ReadonlyException.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/SequenceCursor.class b/classes/uk/ac/man/bioinf/gui/viewer/SequenceCursor.class
new file mode 100644
index 0000000..87d678e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/SequenceCursor.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.class b/classes/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.class
new file mode 100644
index 0000000..fcf7109
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.class b/classes/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.class
new file mode 100644
index 0000000..bb522d4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.class b/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.class
new file mode 100644
index 0000000..bd6f916
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.class b/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.class
new file mode 100644
index 0000000..cb42b85
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.class b/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.class
new file mode 100644
index 0000000..b255719
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.class b/classes/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.class
new file mode 100644
index 0000000..80b60a9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.class
new file mode 100644
index 0000000..f34c297
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.class
new file mode 100644
index 0000000..556cb03
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.class
new file mode 100644
index 0000000..fe63f30
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$1.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$1.class
new file mode 100644
index 0000000..5eb5622
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$1.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$2.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$2.class
new file mode 100644
index 0000000..d48003b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$2.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$3.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$3.class
new file mode 100644
index 0000000..3e2a6c8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$3.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$CursorBlinkThread.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$CursorBlinkThread.class
new file mode 100644
index 0000000..713a3b7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$CursorBlinkThread.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$KeyScroller.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$KeyScroller.class
new file mode 100644
index 0000000..d6ec9a8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$KeyScroller.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$PointListener.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$PointListener.class
new file mode 100644
index 0000000..3cc270c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$PointListener.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$SelectionClearer.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$SelectionClearer.class
new file mode 100644
index 0000000..ecccab1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$SelectionClearer.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$SelectionToggler.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$SelectionToggler.class
new file mode 100644
index 0000000..6f304de
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI$SelectionToggler.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.class
new file mode 100644
index 0000000..0176d35
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.class b/classes/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.class
new file mode 100644
index 0000000..ffa958a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.class b/classes/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.class
new file mode 100644
index 0000000..4ba4ab0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.class b/classes/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.class
new file mode 100644
index 0000000..2a116f7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.class differ
diff --git a/classes/uk/ac/man/bioinf/gui/viewer/test/SliderExample.class b/classes/uk/ac/man/bioinf/gui/viewer/test/SliderExample.class
new file mode 100644
index 0000000..324ec11
Binary files /dev/null and b/classes/uk/ac/man/bioinf/gui/viewer/test/SliderExample.class differ
diff --git a/classes/uk/ac/man/bioinf/io/AlignmentInputParser.class b/classes/uk/ac/man/bioinf/io/AlignmentInputParser.class
new file mode 100644
index 0000000..69c905f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/AlignmentInputParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/AlignmentOutputParser.class b/classes/uk/ac/man/bioinf/io/AlignmentOutputParser.class
new file mode 100644
index 0000000..13e493f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/AlignmentOutputParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.class b/classes/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.class
new file mode 100644
index 0000000..5dbd4f4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.class b/classes/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.class
new file mode 100644
index 0000000..4479219
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.class differ
diff --git a/classes/uk/ac/man/bioinf/io/NarrowedInputStream$NoisyStream.class b/classes/uk/ac/man/bioinf/io/NarrowedInputStream$NoisyStream.class
new file mode 100644
index 0000000..99f1c7a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/NarrowedInputStream$NoisyStream.class differ
diff --git a/classes/uk/ac/man/bioinf/io/NarrowedInputStream.class b/classes/uk/ac/man/bioinf/io/NarrowedInputStream.class
new file mode 100644
index 0000000..6f8bf45
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/NarrowedInputStream.class differ
diff --git a/classes/uk/ac/man/bioinf/io/NullParserExceptionHandler.class b/classes/uk/ac/man/bioinf/io/NullParserExceptionHandler.class
new file mode 100644
index 0000000..17885f0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/NullParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/io/ParserException.class b/classes/uk/ac/man/bioinf/io/ParserException.class
new file mode 100644
index 0000000..3fb01ef
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/ParserException.class differ
diff --git a/classes/uk/ac/man/bioinf/io/ParserExceptionHandler.class b/classes/uk/ac/man/bioinf/io/ParserExceptionHandler.class
new file mode 100644
index 0000000..dfdd9ac
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/ParserExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/io/SequenceInputParser.class b/classes/uk/ac/man/bioinf/io/SequenceInputParser.class
new file mode 100644
index 0000000..052101f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/SequenceInputParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/SequenceWriterException.class b/classes/uk/ac/man/bioinf/io/SequenceWriterException.class
new file mode 100644
index 0000000..acc10df
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/SequenceWriterException.class differ
diff --git a/classes/uk/ac/man/bioinf/io/UnknownElementException.class b/classes/uk/ac/man/bioinf/io/UnknownElementException.class
new file mode 100644
index 0000000..190487f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/UnknownElementException.class differ
diff --git a/classes/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.class b/classes/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.class
new file mode 100644
index 0000000..f04e285
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.class b/classes/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.class
new file mode 100644
index 0000000..2203d15
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.class b/classes/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.class
new file mode 100644
index 0000000..e40ed6b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/parsers/MotProteinParser.class b/classes/uk/ac/man/bioinf/io/parsers/MotProteinParser.class
new file mode 100644
index 0000000..0db44d7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/parsers/MotProteinParser.class differ
diff --git a/classes/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.class b/classes/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.class
new file mode 100644
index 0000000..fff2025
Binary files /dev/null and b/classes/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.class differ
diff --git a/classes/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.class b/classes/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.class
new file mode 100644
index 0000000..45f4219
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/module/DefaultModuleContext.class b/classes/uk/ac/man/bioinf/module/DefaultModuleContext.class
new file mode 100644
index 0000000..f786890
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/DefaultModuleContext.class differ
diff --git a/classes/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.class b/classes/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.class
new file mode 100644
index 0000000..d11a1cd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.class differ
diff --git a/classes/uk/ac/man/bioinf/module/GenericModuleIdentifier.class b/classes/uk/ac/man/bioinf/module/GenericModuleIdentifier.class
new file mode 100644
index 0000000..d751622
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/GenericModuleIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/module/Module.class b/classes/uk/ac/man/bioinf/module/Module.class
new file mode 100644
index 0000000..12ad0d3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/Module.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleContext.class b/classes/uk/ac/man/bioinf/module/ModuleContext.class
new file mode 100644
index 0000000..1a40168
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleContext.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleException.class b/classes/uk/ac/man/bioinf/module/ModuleException.class
new file mode 100644
index 0000000..959e8ad
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleException.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleExceptionType.class b/classes/uk/ac/man/bioinf/module/ModuleExceptionType.class
new file mode 100644
index 0000000..32d5385
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleExceptionType.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleFactoryInstance.class b/classes/uk/ac/man/bioinf/module/ModuleFactoryInstance.class
new file mode 100644
index 0000000..ef5d4b6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleFactoryInstance.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleIdentifier.class b/classes/uk/ac/man/bioinf/module/ModuleIdentifier.class
new file mode 100644
index 0000000..a8e8fe3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleIdentifierList.class b/classes/uk/ac/man/bioinf/module/ModuleIdentifierList.class
new file mode 100644
index 0000000..2d2a9c0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleIdentifierList.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleList.class b/classes/uk/ac/man/bioinf/module/ModuleList.class
new file mode 100644
index 0000000..9cb92a9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleList.class differ
diff --git a/classes/uk/ac/man/bioinf/module/ModuleStorageStructure.class b/classes/uk/ac/man/bioinf/module/ModuleStorageStructure.class
new file mode 100644
index 0000000..ee805ed
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/ModuleStorageStructure.class differ
diff --git a/classes/uk/ac/man/bioinf/module/NoSuchRequiredModule.class b/classes/uk/ac/man/bioinf/module/NoSuchRequiredModule.class
new file mode 100644
index 0000000..f96ea04
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/NoSuchRequiredModule.class differ
diff --git a/classes/uk/ac/man/bioinf/module/NullModuleFactory.class b/classes/uk/ac/man/bioinf/module/NullModuleFactory.class
new file mode 100644
index 0000000..361493e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/module/NullModuleFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/AbstractEditableSequence.class b/classes/uk/ac/man/bioinf/sequence/AbstractEditableSequence.class
new file mode 100644
index 0000000..d64040d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/AbstractEditableSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/AbstractMutableSequence.class b/classes/uk/ac/man/bioinf/sequence/AbstractMutableSequence.class
new file mode 100644
index 0000000..2d2bb4a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/AbstractMutableSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/AbstractSequence.class b/classes/uk/ac/man/bioinf/sequence/AbstractSequence.class
new file mode 100644
index 0000000..f06a041
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/AbstractSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.class b/classes/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.class
new file mode 100644
index 0000000..cf65343
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/DefaultEditableSequence.class b/classes/uk/ac/man/bioinf/sequence/DefaultEditableSequence.class
new file mode 100644
index 0000000..0298b4d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/DefaultEditableSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/DefaultSequence.class b/classes/uk/ac/man/bioinf/sequence/DefaultSequence.class
new file mode 100644
index 0000000..8f21680
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/DefaultSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/EditableSequence.class b/classes/uk/ac/man/bioinf/sequence/EditableSequence.class
new file mode 100644
index 0000000..5ac5fed
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/EditableSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/Element.class b/classes/uk/ac/man/bioinf/sequence/Element.class
new file mode 100644
index 0000000..c0d8e9c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/Element.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/EmptySequence.class b/classes/uk/ac/man/bioinf/sequence/EmptySequence.class
new file mode 100644
index 0000000..92ef5c1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/EmptySequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.class b/classes/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.class
new file mode 100644
index 0000000..72f26e0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/MutableSequence.class b/classes/uk/ac/man/bioinf/sequence/MutableSequence.class
new file mode 100644
index 0000000..ed4e5d6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/MutableSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.class b/classes/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.class
new file mode 100644
index 0000000..eef83dd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/Residue.class b/classes/uk/ac/man/bioinf/sequence/Residue.class
new file mode 100644
index 0000000..22ad276
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/Residue.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/Sequence.class b/classes/uk/ac/man/bioinf/sequence/Sequence.class
new file mode 100644
index 0000000..9794a3e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/Sequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/SequenceException.class b/classes/uk/ac/man/bioinf/sequence/SequenceException.class
new file mode 100644
index 0000000..41a4136
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/SequenceException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/SequenceFactory.class b/classes/uk/ac/man/bioinf/sequence/SequenceFactory.class
new file mode 100644
index 0000000..e96600c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/SequenceFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/SequenceType.class b/classes/uk/ac/man/bioinf/sequence/SequenceType.class
new file mode 100644
index 0000000..ccea8e8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/SequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/Sequences.class b/classes/uk/ac/man/bioinf/sequence/Sequences.class
new file mode 100644
index 0000000..72f9152
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/Sequences.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.class b/classes/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.class
new file mode 100644
index 0000000..13d2248
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.class b/classes/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.class
new file mode 100644
index 0000000..f4c4ba4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.class b/classes/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.class
new file mode 100644
index 0000000..e2bdcf7
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.class b/classes/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.class
new file mode 100644
index 0000000..4664e2a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.class b/classes/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.class
new file mode 100644
index 0000000..155543e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.class b/classes/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.class
new file mode 100644
index 0000000..ff4a55a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.class b/classes/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.class
new file mode 100644
index 0000000..7f6fcdc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/Gap.class b/classes/uk/ac/man/bioinf/sequence/alignment/Gap.class
new file mode 100644
index 0000000..22e733c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/Gap.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/GappedSequence.class b/classes/uk/ac/man/bioinf/sequence/alignment/GappedSequence.class
new file mode 100644
index 0000000..0c22596
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/GappedSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.class b/classes/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.class
new file mode 100644
index 0000000..ff9d8fc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.class b/classes/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.class
new file mode 100644
index 0000000..9c17cdc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.class b/classes/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.class
new file mode 100644
index 0000000..ad3e933
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.class b/classes/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.class
new file mode 100644
index 0000000..6c8d7b2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.class
new file mode 100644
index 0000000..3bec1b2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.class
new file mode 100644
index 0000000..18862d8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.class
new file mode 100644
index 0000000..7c46537
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.class
new file mode 100644
index 0000000..d3222c5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.class
new file mode 100644
index 0000000..fd82ddf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.class
new file mode 100644
index 0000000..90ceb29
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.class
new file mode 100644
index 0000000..17f6026
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.class b/classes/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.class
new file mode 100644
index 0000000..4902a63
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.class b/classes/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.class
new file mode 100644
index 0000000..a84a821
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.class b/classes/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.class
new file mode 100644
index 0000000..a05ea34
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/AbstractModification.class b/classes/uk/ac/man/bioinf/sequence/complex/AbstractModification.class
new file mode 100644
index 0000000..35bff8d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/AbstractModification.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ComplexElement.class b/classes/uk/ac/man/bioinf/sequence/complex/ComplexElement.class
new file mode 100644
index 0000000..944f33f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ComplexElement.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.class
new file mode 100644
index 0000000..28f80a1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.class b/classes/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.class
new file mode 100644
index 0000000..031d07c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ComplexSequence.class b/classes/uk/ac/man/bioinf/sequence/complex/ComplexSequence.class
new file mode 100644
index 0000000..93f1666
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ComplexSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.class b/classes/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.class
new file mode 100644
index 0000000..d96d4c9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.class b/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.class
new file mode 100644
index 0000000..0d100be
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.class b/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.class
new file mode 100644
index 0000000..96ce0a4
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.class b/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.class
new file mode 100644
index 0000000..b7dee50
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence$1.class b/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence$1.class
new file mode 100644
index 0000000..3afa4be
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence$1.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence$DisabledDefaultGappedSequence.class b/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence$DisabledDefaultGappedSequence.class
new file mode 100644
index 0000000..0bad56e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence$DisabledDefaultGappedSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.class b/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.class
new file mode 100644
index 0000000..17ec48c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.class b/classes/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.class
new file mode 100644
index 0000000..8ec8079
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/GenericModification.class b/classes/uk/ac/man/bioinf/sequence/complex/GenericModification.class
new file mode 100644
index 0000000..e9f12f3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/GenericModification.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/HardComplexElementFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/HardComplexElementFactory.class
new file mode 100644
index 0000000..7154988
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/HardComplexElementFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.class
new file mode 100644
index 0000000..348ffe2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.class b/classes/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.class
new file mode 100644
index 0000000..032983a
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/Methylation.class b/classes/uk/ac/man/bioinf/sequence/complex/Methylation.class
new file mode 100644
index 0000000..faf4ba8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/Methylation.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/Modification.class b/classes/uk/ac/man/bioinf/sequence/complex/Modification.class
new file mode 100644
index 0000000..d24ba3e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/Modification.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ModificationFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/ModificationFactory.class
new file mode 100644
index 0000000..30127b5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ModificationFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ModificationSet$1.class b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSet$1.class
new file mode 100644
index 0000000..79156a6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSet$1.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ModificationSet.class b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSet.class
new file mode 100644
index 0000000..13d34d0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSet.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ModificationSetFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSetFactory.class
new file mode 100644
index 0000000..10be7d3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSetFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.class b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.class
new file mode 100644
index 0000000..87eff22
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.class b/classes/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.class
new file mode 100644
index 0000000..0a9c192
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/SingletonModification.class b/classes/uk/ac/man/bioinf/sequence/complex/SingletonModification.class
new file mode 100644
index 0000000..5962957
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/SingletonModification.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/WeakComplexElementFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/WeakComplexElementFactory.class
new file mode 100644
index 0000000..fe19e1d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/WeakComplexElementFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.class b/classes/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.class
new file mode 100644
index 0000000..83dd766
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/SequenceEvent.class b/classes/uk/ac/man/bioinf/sequence/event/SequenceEvent.class
new file mode 100644
index 0000000..7c9a879
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/SequenceEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.class b/classes/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.class
new file mode 100644
index 0000000..f3e9008
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/SequenceEventType.class b/classes/uk/ac/man/bioinf/sequence/event/SequenceEventType.class
new file mode 100644
index 0000000..a8b5f52
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/SequenceEventType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/SequenceListener.class b/classes/uk/ac/man/bioinf/sequence/event/SequenceListener.class
new file mode 100644
index 0000000..967f17f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/SequenceListener.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.class b/classes/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.class
new file mode 100644
index 0000000..9c1211c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/SequenceVetoException.class b/classes/uk/ac/man/bioinf/sequence/event/SequenceVetoException.class
new file mode 100644
index 0000000..8b27dbc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/SequenceVetoException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.class b/classes/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.class
new file mode 100644
index 0000000..fc5dc2e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.class b/classes/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.class
new file mode 100644
index 0000000..c8cade0
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.class b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.class
new file mode 100644
index 0000000..88efa74
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.class b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.class
new file mode 100644
index 0000000..0fa6cdb
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.class b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.class
new file mode 100644
index 0000000..06bdb90
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.class b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.class
new file mode 100644
index 0000000..13f2cb6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.class b/classes/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.class
new file mode 100644
index 0000000..bee6ac1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.class b/classes/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.class
new file mode 100644
index 0000000..f0bfcfc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.class b/classes/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.class
new file mode 100644
index 0000000..92a061e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment$1.class b/classes/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment$1.class
new file mode 100644
index 0000000..5a9f7cf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment$1.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.class b/classes/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.class
new file mode 100644
index 0000000..c47c966
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/group/SequenceGroup.class b/classes/uk/ac/man/bioinf/sequence/group/SequenceGroup.class
new file mode 100644
index 0000000..4d24eb5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/group/SequenceGroup.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.class b/classes/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.class
new file mode 100644
index 0000000..df74f34
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.class b/classes/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.class
new file mode 100644
index 0000000..18684b2
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/FileSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/FileSource.class
new file mode 100644
index 0000000..792ed34
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/FileSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/Identifiable.class b/classes/uk/ac/man/bioinf/sequence/identifier/Identifiable.class
new file mode 100644
index 0000000..afe3ba9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/Identifiable.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/Identifier.class b/classes/uk/ac/man/bioinf/sequence/identifier/Identifier.class
new file mode 100644
index 0000000..895a11c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/Identifier.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.class b/classes/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.class
new file mode 100644
index 0000000..5bc4727
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.class b/classes/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.class
new file mode 100644
index 0000000..18d02e5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/NoSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/NoSource.class
new file mode 100644
index 0000000..6caddd1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/NoSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/ReaderSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/ReaderSource.class
new file mode 100644
index 0000000..198b8da
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/ReaderSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/SequenceSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/SequenceSource.class
new file mode 100644
index 0000000..e57e1cb
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/SequenceSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.class b/classes/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.class
new file mode 100644
index 0000000..1662fb9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/SimpleSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/SimpleSource.class
new file mode 100644
index 0000000..ef14968
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/SimpleSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/Source.class b/classes/uk/ac/man/bioinf/sequence/identifier/Source.class
new file mode 100644
index 0000000..b857618
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/Source.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.class
new file mode 100644
index 0000000..d6ddbf3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.class b/classes/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.class
new file mode 100644
index 0000000..36a6d7b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.class b/classes/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.class
new file mode 100644
index 0000000..0b130aa
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/AbstractElement.class b/classes/uk/ac/man/bioinf/sequence/types/AbstractElement.class
new file mode 100644
index 0000000..56544d5
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/AbstractElement.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.class b/classes/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.class
new file mode 100644
index 0000000..47a5c6f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.class b/classes/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.class
new file mode 100644
index 0000000..9e0c224
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/AminoAcid.class b/classes/uk/ac/man/bioinf/sequence/types/AminoAcid.class
new file mode 100644
index 0000000..3e2c50f
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/AminoAcid.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/DNANucleotide.class b/classes/uk/ac/man/bioinf/sequence/types/DNANucleotide.class
new file mode 100644
index 0000000..2c74139
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/DNANucleotide.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/DNAResidue.class b/classes/uk/ac/man/bioinf/sequence/types/DNAResidue.class
new file mode 100644
index 0000000..fd0e3a1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/DNAResidue.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/DNASequenceType.class b/classes/uk/ac/man/bioinf/sequence/types/DNASequenceType.class
new file mode 100644
index 0000000..4c0e6c8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/DNASequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/EmptySequenceType.class b/classes/uk/ac/man/bioinf/sequence/types/EmptySequenceType.class
new file mode 100644
index 0000000..f94be6c
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/EmptySequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/NucleotideResidue.class b/classes/uk/ac/man/bioinf/sequence/types/NucleotideResidue.class
new file mode 100644
index 0000000..5f9ba30
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/NucleotideResidue.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/ProteinResidue.class b/classes/uk/ac/man/bioinf/sequence/types/ProteinResidue.class
new file mode 100644
index 0000000..7d3bc06
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/ProteinResidue.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.class b/classes/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.class
new file mode 100644
index 0000000..bea13f8
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/RNANucleotide.class b/classes/uk/ac/man/bioinf/sequence/types/RNANucleotide.class
new file mode 100644
index 0000000..f7f5755
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/RNANucleotide.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/RNAResidue.class b/classes/uk/ac/man/bioinf/sequence/types/RNAResidue.class
new file mode 100644
index 0000000..51683bd
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/RNAResidue.class differ
diff --git a/classes/uk/ac/man/bioinf/sequence/types/RNASequenceType.class b/classes/uk/ac/man/bioinf/sequence/types/RNASequenceType.class
new file mode 100644
index 0000000..07a8756
Binary files /dev/null and b/classes/uk/ac/man/bioinf/sequence/types/RNASequenceType.class differ
diff --git a/classes/uk/ac/man/bioinf/util/AbstractEnumeration$ElementIterator.class b/classes/uk/ac/man/bioinf/util/AbstractEnumeration$ElementIterator.class
new file mode 100644
index 0000000..a5002d9
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/AbstractEnumeration$ElementIterator.class differ
diff --git a/classes/uk/ac/man/bioinf/util/AbstractEnumeration.class b/classes/uk/ac/man/bioinf/util/AbstractEnumeration.class
new file mode 100644
index 0000000..a7d8425
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/AbstractEnumeration.class differ
diff --git a/classes/uk/ac/man/bioinf/util/ArrayManipulation.class b/classes/uk/ac/man/bioinf/util/ArrayManipulation.class
new file mode 100644
index 0000000..9fab3e1
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/ArrayManipulation.class differ
diff --git a/classes/uk/ac/man/bioinf/util/Changeable.class b/classes/uk/ac/man/bioinf/util/Changeable.class
new file mode 100644
index 0000000..2a36cdc
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/Changeable.class differ
diff --git a/classes/uk/ac/man/bioinf/util/ChangeableEvent.class b/classes/uk/ac/man/bioinf/util/ChangeableEvent.class
new file mode 100644
index 0000000..57a703d
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/ChangeableEvent.class differ
diff --git a/classes/uk/ac/man/bioinf/util/ChangeableListener.class b/classes/uk/ac/man/bioinf/util/ChangeableListener.class
new file mode 100644
index 0000000..c5f45fb
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/ChangeableListener.class differ
diff --git a/classes/uk/ac/man/bioinf/util/ChangeableListenerSupport.class b/classes/uk/ac/man/bioinf/util/ChangeableListenerSupport.class
new file mode 100644
index 0000000..117c562
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/ChangeableListenerSupport.class differ
diff --git a/classes/uk/ac/man/bioinf/util/CollectionPrinter.class b/classes/uk/ac/man/bioinf/util/CollectionPrinter.class
new file mode 100644
index 0000000..f8b1dec
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/CollectionPrinter.class differ
diff --git a/classes/uk/ac/man/bioinf/util/Direction.class b/classes/uk/ac/man/bioinf/util/Direction.class
new file mode 100644
index 0000000..d232052
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/Direction.class differ
diff --git a/classes/uk/ac/man/bioinf/util/ExceptionHandler.class b/classes/uk/ac/man/bioinf/util/ExceptionHandler.class
new file mode 100644
index 0000000..8ef80f6
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/ExceptionHandler.class differ
diff --git a/classes/uk/ac/man/bioinf/util/IntArrayList.class b/classes/uk/ac/man/bioinf/util/IntArrayList.class
new file mode 100644
index 0000000..e092b97
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/IntArrayList.class differ
diff --git a/classes/uk/ac/man/bioinf/util/PackageResourceAdapter.class b/classes/uk/ac/man/bioinf/util/PackageResourceAdapter.class
new file mode 100644
index 0000000..b3914bf
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/PackageResourceAdapter.class differ
diff --git a/classes/uk/ac/man/bioinf/util/ResourceAdapter.class b/classes/uk/ac/man/bioinf/util/ResourceAdapter.class
new file mode 100644
index 0000000..557595e
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/ResourceAdapter.class differ
diff --git a/classes/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.class b/classes/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.class
new file mode 100644
index 0000000..f1c8514
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.class differ
diff --git a/classes/uk/ac/man/bioinf/util/SwingWorker$1.class b/classes/uk/ac/man/bioinf/util/SwingWorker$1.class
new file mode 100644
index 0000000..f1058a3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/SwingWorker$1.class differ
diff --git a/classes/uk/ac/man/bioinf/util/SwingWorker$2.class b/classes/uk/ac/man/bioinf/util/SwingWorker$2.class
new file mode 100644
index 0000000..ee26884
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/SwingWorker$2.class differ
diff --git a/classes/uk/ac/man/bioinf/util/SwingWorker$ThreadVar.class b/classes/uk/ac/man/bioinf/util/SwingWorker$ThreadVar.class
new file mode 100644
index 0000000..24b266b
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/SwingWorker$ThreadVar.class differ
diff --git a/classes/uk/ac/man/bioinf/util/SwingWorker.class b/classes/uk/ac/man/bioinf/util/SwingWorker.class
new file mode 100644
index 0000000..6044ff3
Binary files /dev/null and b/classes/uk/ac/man/bioinf/util/SwingWorker.class differ
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index fb6c9f6..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,6 +0,0 @@
-cinema for Debian
------------------
-
-Cinema is a dependency for mauve. This shall just work.
-
- -- Steffen Moeller <moeller at debian.org> Tue, 07 Jun 2011 18:40:09 +0200
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index e8d40bf..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,9 +0,0 @@
-cinema (3.0.23-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
-
- [ Thorsten Alteholz ]
- * debian/get-orig-source: put orig.tar.gz in ../tarballs to allow
- automatic build with svn-buildpackage
-
- -- Steffen Moeller <moeller at debian.org> Tue, 07 Jun 2011 18:40:09 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index f599e28..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-10
diff --git a/debian/control b/debian/control
deleted file mode 100644
index a124cb5..0000000
--- a/debian/control
+++ /dev/null
@@ -1,22 +0,0 @@
-Source: cinema
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 3.9.8
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cinema/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/cinema/trunk
-Homepage: http://aig.cs.man.ac.uk/research/utopia/cinema/cinema.php
-
-Package: cinema
-Architecture: all
-Depends: ${misc:Depends}
-Description: multi-sequence alignment editor and viewer
- It has been designed to be as extensible as possible. Notes of this
- extensibility can be found in "EXTENDING_CINEMA", and the
- "cinema-module" sub-directory.
- .
- Cinema currently has limited support for various sequence formats,
- although its easy to add new ones. A large number of alignments in the
- appropriate format can be found as part of the align compendium at
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index ab0aac7..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,32 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: cinema
-Source: http://homepages.cs.ncl.ac.uk/phillip.lord/download/java/cinema/cinema-3_0_23.tar.gz
-
-Files: *
-Copyright: <years> <put author's name and email here>
- <years> <likewise for another author>
-License: LGPL
-
-# If you want to use GPL v2 or later for the /debian/* files use
-# the following clauses, or change it to suit. Delete these two lines
-Files: debian/*
-Copyright: 2011 Steffen Moeller <moeller at debian.org>
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index e845566..0000000
--- a/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-README
diff --git a/debian/patches/ant.patch b/debian/patches/ant.patch
deleted file mode 100644
index c0daafc..0000000
--- a/debian/patches/ant.patch
+++ /dev/null
@@ -1,265 +0,0 @@
-Index: cinema-3.0.23/src/uk/ac/man/bioinf/build.xml
-===================================================================
---- cinema-3.0.23.orig/src/uk/ac/man/bioinf/build.xml 2011-06-07 19:37:22.000000000 +0200
-+++ cinema-3.0.23/src/uk/ac/man/bioinf/build.xml 2011-06-07 19:37:56.000000000 +0200
-@@ -57,7 +57,7 @@
- <property name="javadoc.packages" value="uk.ac.man.bioinf.*" />
-
- <!-- Support for texi doclet. Set the first to use -->
-- <property name="javadoc.use.texidoc"/>
-+ <property name="javadoc.use.texidoc" value="." />
- <property name="javadoc.texidoc.path" value="."/>
- <property name="javadoc.texi" value="${javadoc}" />
-
-@@ -91,6 +91,9 @@
- <fileset dir="${ext}">
- <include name="**/*.jar" />
- </fileset>
-+ <fileset dir="/usr/share/java">
-+ <include name="**/*.jar" />
-+ </fileset>
-
- </path>
-
-@@ -108,6 +111,7 @@
- <javac classpathref="project.class.path"
- debug="${debug}"
- srcdir="${src}"
-+ source="1.4"
- destdir="${classes}">
- <include name="uk/**/*.java" />
- <exclude name="${exclude}" />
-@@ -327,7 +331,3 @@
- <target name="all" description="Build everything from scratch"
- depends="clean,prepare,dist_build,javadoc" />
- </project>
--
--
--
--
-\ No newline at end of file
-Index: cinema-3.0.23/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java
-===================================================================
---- cinema-3.0.23.orig/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java 2011-06-07 19:38:20.000000000 +0200
-+++ /dev/null 1970-01-01 00:00:00.000000000 +0000
-@@ -1,96 +0,0 @@
--/*
-- * This program is free software; you can redistribute it and/or modify
-- * it under the terms of the GNU General Public License as published by
-- * the Free Software Foundation; either version 2 of the License, or
-- * (at your option) any later version.
-- *
-- * This program is distributed in the hope that it will be useful,
-- * but WITHOUT ANY WARRANTY; without even the implied warranty of
-- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-- * GNU General Public License for more details.
-- *
-- * You should have received a copy of the GNU General Public License
-- * along with this program; if not, write to the Free Software
-- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
--*/
--
--/*
-- * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
-- * whilst at the University of Manchester as a Pfizer post-doctoral
-- * Research Fellow.
-- *
-- * The initial code base is copyright by Pfizer, or the University
-- * of Manchester. Modifications to the initial code base are copyright
-- * of their respective authors, or their employers as appropriate.
-- * Authorship of the modifications may be determined from the ChangeLog
-- * placed at the end of this file
-- */
--
--package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
--import org.xml.sax.InputSource;
--import org.xml.sax.SAXException;
--import org.xml.sax.XMLReader;
--import org.xml.sax.helpers.DefaultHandler;
--import org.xml.sax.helpers.XMLReaderFactory;
--import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
--import uk.ac.man.bioinf.apps.xml.XMLParserFactory;
--import uk.ac.man.bioinf.debug.Debug;
--
--
--/**
-- * CinemaXMLParserFactory.java
-- *
-- *
-- * Created: Mon Sep 18 18:59:17 2000
-- *
-- * @author Phillip Lord
-- * @version $Id: CinemaXMLParserFactory.java,v 1.3 2001/04/11 17:04:41 lord Exp $
-- */
--
--public class CinemaXMLParserFactory implements XMLParserFactory
--{
--
-- public XMLReader getXMLParser()
-- {
-- try{
--
-- XMLReader read = XMLReaderFactory.createXMLReader( "org.apache.xerces.parsers.SAXParser" );
-- read.setEntityResolver
-- ( new DefaultHandler(){
-- public InputSource resolveEntity( String publicId, String systemId ) throws SAXException
-- {
-- if( systemId.equals( "file:module.dtd" ) ){
-- return new InputSource( CinemaResources.getModuleDTDAsResource() );
-- }
--
-- return super.resolveEntity( publicId, systemId );
-- }
-- });
-- return read;
-- }
-- catch( Exception exp ){
-- if( Debug.debug )
-- Debug.throwable( this, exp );
-- }
-- return null;
-- }
--} // CinemaXMLParserFactory
--
--
--
--/*
-- * ChangeLog
-- * $Log: CinemaXMLParserFactory.java,v $
-- * Revision 1.3 2001/04/11 17:04:41 lord
-- * Added License agreements to all code
-- *
-- * Revision 1.2 2000/12/18 12:09:23 jns
-- * o getting rid of system.out.println to avoid noisy output out of debug
-- * mode
-- *
-- * Revision 1.1 2000/09/25 16:35:34 lord
-- * Changes made so that the XMLParser used is no longer hard coded
-- * but comes from a factory. This allows for instance giving the parser a
-- * custom entity resolver.
-- *
-- */
-Index: cinema-3.0.23/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java
-===================================================================
---- cinema-3.0.23.orig/home/moeller/alioth/debian-med/packages/cinema/cinema-3.0.23/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java 2011-06-07 19:38:40.000000000 +0200
-+++ /dev/null 1970-01-01 00:00:00.000000000 +0000
-@@ -1,119 +0,0 @@
--/*
-- *This library is free software; you can redistribute it and/or
-- *modify it under the terms of the GNU Lesser General Public
-- *License as published by the Free Software Foundation; either
-- *version 2.1 of the License, or (at your option) any later version.
-- *
-- *This library is distributed in the hope that it will be useful,
-- *but WITHOUT ANY WARRANTY; without even the implied warranty of
-- *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-- *Lesser General Public License for more details.
-- *
-- *You should have received a copy of the GNU Lesser General Public
-- *License along with this library; if not, write to the Free Software
-- *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
--*/
--
--/*
-- * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
-- * whilst at the University of Manchester as a Pfizer post-doctoral
-- * Research Fellow.
-- *
-- * The initial code base is copyright by Pfizer, or the University
-- * of Manchester. Modifications to the initial code base are copyright
-- * of their respective authors, or their employers as appropriate.
-- * Authorship of the modifications may be determined from the ChangeLog
-- * placed at the end of this file
-- */
--
--package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
--import org.xml.sax.InputSource;
--import org.xml.sax.SAXException;
--import org.xml.sax.XMLReader;
--import org.xml.sax.helpers.DefaultHandler;
--import org.xml.sax.helpers.XMLReaderFactory;
--import uk.ac.man.bioinf.debug.Debug;
--
--
--/**
-- * DefaultXMLParser.java
-- *
-- *
-- * Created: Mon May 8 21:08:32 2000
-- *
-- * @author Phillip Lord
-- * @version $Id: DefaultXMLParser.java,v 1.5 2001/04/11 17:04:42 lord Exp $
-- */
--
--public class DefaultXMLParser implements XMLParserFactory
--{
-- public XMLReader getXMLParser()
-- {
-- try{
-- XMLReader read = XMLReaderFactory.createXMLReader( "org.apache.xerces.parsers.SAXParser" );
-- read.setEntityResolver
-- ( new DefaultHandler(){
-- public InputSource resolveEntity( String publicId, String systemId ) throws SAXException
-- {
-- InputSource retn = super.resolveEntity( publicId, systemId );
-- System.out.println( "ENTITY:- " + retn + " pub " + publicId + " sys " + systemId );
-- return retn;
-- }
-- });
-- return read;
-- }
-- catch( Exception exp ){
-- if( Debug.debug )
-- Debug.throwable( this, exp );
-- }
-- return null;
-- }
--} // DefaultXMLParser
--
--
--
--/*
-- * ChangeLog
-- * $Log: DefaultXMLParser.java,v $
-- * Revision 1.5 2001/04/11 17:04:42 lord
-- * Added License agreements to all code
-- *
-- * Revision 1.4 2000/12/18 12:12:53 jns
-- * o getting rid of system.out.println to avoid noisy output out of debug
-- * mode
-- *
-- * Revision 1.3 2000/10/19 17:51:15 lord
-- * Import rationalisation
-- *
-- * Revision 1.2 2000/09/25 16:35:34 lord
-- * Changes made so that the XMLParser used is no longer hard coded
-- * but comes from a factory. This allows for instance giving the parser a
-- * custom entity resolver.
-- *
-- * Revision 1.1 2000/05/15 16:23:53 lord
-- * Initial checkin
-- *
-- */
--
--/*
-- * ChangeLog
-- * $Log: DefaultXMLParser.java,v $
-- * Revision 1.5 2001/04/11 17:04:42 lord
-- * Added License agreements to all code
-- *
-- * Revision 1.4 2000/12/18 12:12:53 jns
-- * o getting rid of system.out.println to avoid noisy output out of debug
-- * mode
-- *
-- * Revision 1.3 2000/10/19 17:51:15 lord
-- * Import rationalisation
-- *
-- * Revision 1.2 2000/09/25 16:35:34 lord
-- * Changes made so that the XMLParser used is no longer hard coded
-- * but comes from a factory. This allows for instance giving the parser a
-- * custom entity resolver.
-- *
-- * Revision 1.1 2000/05/15 16:23:53 lord
-- * Initial checkin
-- *
-- */
diff --git a/debian/patches/application.patch b/debian/patches/application.patch
deleted file mode 100644
index 95e7440..0000000
--- a/debian/patches/application.patch
+++ /dev/null
@@ -1,52 +0,0 @@
-Index: cinema-3.0.23/bin/cinema
-===================================================================
---- cinema-3.0.23.orig/bin/cinema 2011-06-07 19:41:52.000000000 +0200
-+++ cinema-3.0.23/bin/cinema 2011-06-07 20:12:19.000000000 +0200
-@@ -16,6 +16,7 @@
- ## to this is probably to do as much of the command liner parsing in
- ## Java as possible.
-
-+set -e
-
- ## This is the location of the main install directory where Cinema
- ## should find all most of its jar files.
-@@ -66,8 +67,15 @@
- ext_jars=${ext_jars}:$jar_file
- done
-
-+#for jar_file in $( find /usr/share/java/ -name "*.jar" -a ! -type l )
-+for jar_file in /usr/share/java/gnu-getopt.jar /usr/share/java/regexp.jar /usr/share/java/xalan2.jar /usr/share/java/nekohtml.jar /usr/share/java/nekohtmlXni.jar
-+do
-+ [ -r $jar_file ] || echo "Not found: $jar_file"
-+ system_jars=${system_jars}:$jar_file
-+done
-+
- # classpath
--classpath=${user_jars}${cinema_jars}${ext_jars}
-+classpath=${user_jars}${cinema_jars}${ext_jars}:${system_jars}
-
-
- ##
-@@ -81,4 +89,5 @@
- echo "Running Cinema as ${COMMAND_LINE}"
- fi
-
-+echo "executing java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS $*"
- java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS $*
-Index: cinema-3.0.23/bin/cinema.pl
-===================================================================
---- cinema-3.0.23.orig/bin/cinema.pl 2011-06-07 19:43:56.000000000 +0200
-+++ cinema-3.0.23/bin/cinema.pl 2011-06-07 19:44:32.000000000 +0200
-@@ -63,7 +63,11 @@
- $ext_jars.=":$jarfile";
- }
-
--my $classpath="$user_jars$cinema_jars$ext_jars";
-+foreach $jarfile ( glob( "/usr/share/java/*jar" ) ){
-+ $system_jars.=":$jarfile";
-+}
-+
-+my $classpath="$user_jars$cinema_jars$ext_jars$system_jars";
-
- if( $VERBOSE ){
- print "java -classpath $classpath $JVM_OPTIONS uk.ac.man.bioinf.apps.cinema.Cinema @ARGV";
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 6ff84be..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1,3 +0,0 @@
-ant.patch
-application.patch
-ioexception.patch
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 63756db..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,27 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# debian/rules for cinema
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
- dh $@
-
-dh_override_auto_build:
- mkdir -p classes/ext
- cd src/uk/ac/man/bioinf && ant dist_build
-
-
-get-orig-source:
- # this version is mostly historical
- [ -r cinema-3_0_23.tar.gz ] || wget http://homepages.cs.ncl.ac.uk/phillip.lord/download/java/cinema/cinema-3_0_23.tar.gz
- tar xzvf cinema-3_0_23.tar.gz
- cd cinema-3_0_23 && rm -r classes lib
- mv cinema-3_0_23 cinema-3.0.23
- tar czvf cinema_3.0.23.orig.tar.gz cinema-3.0.23
- rm -r cinema-3.0.23
- rm cinema-3_0_23.tar.gz
- # put orig.tar in ../tarballs (-> default location for svn-buildpackage)
- mkdir -p ../tarballs
- mv *orig.tar.gz ../tarballs
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index ec83afb..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=3
-opts="uversionmangle=s/_/./g" \
-http://homepages.cs.ncl.ac.uk/phillip.lord/download/java/cinema/cinema-([0-9_]+).tar.gz
diff --git a/doc/ASL b/doc/ASL
new file mode 100644
index 0000000..9bafae1
--- /dev/null
+++ b/doc/ASL
@@ -0,0 +1,58 @@
+* ====================================================================
+ * The Apache Software License, Version 1.1
+ *
+ * Copyright (c) 2000 The Apache Software Foundation. All rights
+ * reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions
+ * are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright
+ * notice, this list of conditions and the following disclaimer.
+ *
+ * 2. Redistributions in binary form must reproduce the above copyright
+ * notice, this list of conditions and the following disclaimer in
+ * the documentation and/or other materials provided with the
+ * distribution.
+ *
+ * 3. The end-user documentation included with the redistribution,
+ * if any, must include the following acknowledgment:
+ * "This product includes software developed by the
+ * Apache Software Foundation (http://www.apache.org/)."
+ * Alternately, this acknowledgment may appear in the software itself,
+ * if and wherever such third-party acknowledgments normally appear.
+ *
+ * 4. The names "Apache" and "Apache Software Foundation" must
+ * not be used to endorse or promote products derived from this
+ * software without prior written permission. For written
+ * permission, please contact apache at apache.org.
+ *
+ * 5. Products derived from this software may not be called "Apache",
+ * nor may "Apache" appear in their name, without prior written
+ * permission of the Apache Software Foundation.
+ *
+ * THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED OR IMPLIED
+ * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
+ * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION OR
+ * ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
+ * USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ * SUCH DAMAGE.
+ * ====================================================================
+ *
+ * This software consists of voluntary contributions made by many
+ * individuals on behalf of the Apache Software Foundation. For more
+ * information on the Apache Software Foundation, please see
+ * <http://www.apache.org/>.
+ *
+ * Portions of this software are based upon public domain software
+ * originally written at the National Center for Supercomputing Applications,
+ * University of Illinois, Urbana-Champaign.
+ */
+
diff --git a/doc/AUTHORS b/doc/AUTHORS
new file mode 100644
index 0000000..fc8cce1
--- /dev/null
+++ b/doc/AUTHORS
@@ -0,0 +1,15 @@
+
+
+
+Primary Authors
+
+ Phillip Lord (p.lord at hgmp.mrc.ac.uk), School of Biological Sciences, Manchester
+ Crispin Miller (c.miller at cs.man.ac.uk), Computing Science, Manchester
+ Julian Selley, (j.selley at man.ac.uk), School of Biological Sciences, Manchester
+
+
+
+
+Authorship of the various segments of code can largely be determined
+from the change logs and comments found within the code.
+
diff --git a/doc/CINEMA b/doc/CINEMA
new file mode 100644
index 0000000..9a7fe1a
--- /dev/null
+++ b/doc/CINEMA
@@ -0,0 +1,13 @@
+Cinema-mx is a multi-sequence alignment editor and viewer.
+
+It has been designed to be as extensible as possible. Notes of this
+extensibility can be found in "EXTENDING_CINEMA", and the
+"cinema-module" sub-directory.
+
+Cinema currently has limited support for various sequence formats,
+although its easy to add new ones. A large number of alignments in the
+appropriate format can be found as part of the align compendium at
+
+http://www.bioinf.man.ac.uk/dbbrowser/ALIGN/
+
+
diff --git a/doc/EXTENDING_CINEMA b/doc/EXTENDING_CINEMA
new file mode 100644
index 0000000..7bbc6d3
--- /dev/null
+++ b/doc/EXTENDING_CINEMA
@@ -0,0 +1,17 @@
+Cinema-MX was written to be extensible. So how do you extend it?
+
+The actual MX architecture is described elsewhere, in a file called
+"cinema-module". You will need to read this, if you want to understand
+this.
+
+Cinema allows extension using the MX architecture. Two directories are
+important for this, both within the ~/.cinema directory. Assuming that
+you have installed cinema using the hard installation method, then any
+jar files added into the ~/.cinema/ext directory will be added into
+the classpath, so that you can access them. Secondly in the directory
+~/.cinema/config directory the file "main.xml" will be loaded (if it
+exists). Any other files in this directory can also be loaded using
+the "load" directive, if you want to modularlise your configuration.
+
+The final directory ~/.cinema/persist is used by Cinema to maintain
+state information.
\ No newline at end of file
diff --git a/doc/INSTALL b/doc/INSTALL
new file mode 100644
index 0000000..1975264
--- /dev/null
+++ b/doc/INSTALL
@@ -0,0 +1,106 @@
+INSTALLATION INSTRUCTIONS FOR CINEMA-MX
+
+The following instructions assume that Java has already been
+installed. If it has not then this should be done first.
+
+
+EASY INSTRUCTIONS.
+
+
+There are two ways to run Cinema, one easier than the other. The easy
+way will be presented first and then the harder way. Why are there two
+ways? If you want to know this, then I suggest that you read the hard
+way....
+
+
+Windows.
+
+1) Unpack the archive file. If you are reading this, then there is a
+ fairly good chance that you have already achieved this.
+
+2) Move to the cinema-XX/lib directory (where XX is the version name
+ whatever it is).
+
+3) Click on cinema.jar. You can also drag a shortcut to the desktop,
+ and click on that.
+
+4) If you are using a command line then "java -jar
+ cinema.jar" will achieve the same end. If the click and point
+ technique doesn't work this is a good thing to try as it will
+ probably give you error messages.
+
+
+UNIX Installation
+
+1) Unpack the archive file. If you are reading this, there is a good
+ chance that you have already done this.
+
+2) Move into the cinema-XX/bin directory, and type "./cinema"
+
+3) If you use a graphical launcher such as GNOME or KDE, then you can
+ use the same command line, setting the directory appropriately.
+
+4) If you want to install system wide, I'd suggest you use the hard
+ installation. Also if you want to launch Cinema from another directory.
+
+
+HARD INSTALLATION.
+
+The hard installation isn't really the hard, and more over its
+better. The reason that I've provided it is that its better. One of
+the point with CINEMA is that its easily to extend. You can add new
+modules if you like. But to do this you have to make these modules
+available to Java, in the class path. The hard method uses a shell
+script which works automatically does this. In particular any jar
+files in the ~/.cinema/ext directory will be added into the class
+path.
+
+It would be nice to get this working through Java, rather than using a
+shell script. But I struggled for several days trying to extend the
+classpath in a running JVM, and failed miserably. I'm sure its
+possible. Anyone telling me how will to do this will recieve a nice
+"thank you" email. Anyone sending me example code, will get a place in
+the Acknowledgement file.
+
+
+UNIX installation.
+
+1) Unpack the archive file in the directory where you wish to
+install. There are several obvious locations to do this, depending on
+your local installation. I would use ~/bin (for a personal
+installation), or one of /opt, or /usr/lib, or /usr/local/lib/
+
+2) (Optional) Unpacking will leave a directory with a version number
+in it. I normally put a symlink in to this directory without the
+version number. It makes it easier to have several versions available
+at once.
+
+3) Either put the bin/ directory into your system path, or symlink
+the bin/cinema file into a directory in your system path.
+
+4) Edit the cinema file. Change the line
+CINEMA_LIB=../lib to point to the lib/ directory. Until you do this
+cinema will have to be launched from the bin/ directory, which is a
+pain.
+
+5) Thats it.
+
+
+Windows.
+
+If you have cygwin installed (if you don't know, you haven't.)
+
+1) Unpack the distribution file.
+
+2) Edit the cinema.cygwin, so that the CINEMA_LIB line points to the
+lib/ directory.
+
+3) Symlink cinema.cygwin into your system path.
+
+4) Thats it.
+
+If you don't have cygwin installed, you can install it, or you can try
+the perl file if you have perl installed. At some point I would like
+to write a .bat file to do this. If you want the extensibility then I
+suggest you write a .bat file, and add any jar files in by hand. You
+can copy the command line from the shell script.
diff --git a/doc/LGPL b/doc/LGPL
new file mode 100644
index 0000000..0e450eb
--- /dev/null
+++ b/doc/LGPL
@@ -0,0 +1,311 @@
+
+
+GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 2.1, February 1999
+
+Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+Everyone is permitted to copy and distribute verbatim copies
+of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+Preamble
+
+The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU
+General Public Licenses are intended to guarantee your freedom to share and change free software--to make sure the
+software is free for all its users.
+
+This license, the Lesser General Public License, applies to some specially designated software packages--typically
+libraries--of the Free Software Foundation and other authors who decide to use it. You can use it too, but we suggest you
+first think carefully about whether this license or the ordinary General Public License is the better strategy to use in any
+particular case, based on the explanations below.
+
+When we speak of free software, we are referring to freedom of use, not price. Our General Public Licenses are designed to
+make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish); that you
+receive source code or can get it if you want it; that you can change the software and use pieces of it in new free programs;
+and that you are informed that you can do these things.
+
+To protect your rights, we need to make restrictions that forbid distributors to deny you these rights or to ask you to
+surrender these rights. These restrictions translate to certain responsibilities for you if you distribute copies of the library
+or if you modify it.
+
+For example, if you distribute copies of the library, whether gratis or for a fee, you must give the recipients all the rights
+that we gave you. You must make sure that they, too, receive or can get the source code. If you link other code with the
+library, you must provide complete object files to the recipients, so that they can relink them with the library after making
+changes to the library and recompiling it. And you must show them these terms so they know their rights.
+
+We protect your rights with a two-step method: (1) we copyright the library, and (2) we offer you this license, which gives
+you legal permission to copy, distribute and/or modify the library.
+
+To protect each distributor, we want to make it very clear that there is no warranty for the free library. Also, if the library
+is modified by someone else and passed on, the recipients should know that what they have is not the original version, so
+that the original author's reputation will not be affected by problems that might be introduced by others.
+
+Finally, software patents pose a constant threat to the existence of any free program. We wish to make sure that a company
+cannot effectively restrict the users of a free program by obtaining a restrictive license from a patent holder. Therefore, we
+insist that any patent license obtained for a version of the library must be consistent with the full freedom of use specified
+in this license.
+
+Most GNU software, including some libraries, is covered by the ordinary GNU General Public License. This license, the
+GNU Lesser General Public License, applies to certain designated libraries, and is quite different from the ordinary
+General Public License. We use this license for certain libraries in order to permit linking those libraries into non-free
+programs.
+
+When a program is linked with a library, whether statically or using a shared library, the combination of the two is legally
+speaking a combined work, a derivative of the original library. The ordinary General Public License therefore permits such
+linking only if the entire combination fits its criteria of freedom. The Lesser General Public License permits more lax
+criteria for linking other code with the library.
+
+We call this license the "Lesser" General Public License because it does Less to protect the user's freedom than the
+ordinary General Public License. It also provides other free software developers Less of an advantage over competing
+non-free programs. These disadvantages are the reason we use the ordinary General Public License for many libraries.
+However, the Lesser license provides advantages in certain special circumstances.
+
+For example, on rare occasions, there may be a special need to encourage the widest possible use of a certain library, so that
+it becomes a de-facto standard. To achieve this, non-free programs must be allowed to use the library. A more frequent
+case is that a free library does the same job as widely used non-free libraries. In this case, there is little to gain by limiting
+the free library to free software only, so we use the Lesser General Public License.
+
+In other cases, permission to use a particular library in non-free programs enables a greater number of people to use a large
+body of free software. For example, permission to use the GNU C Library in non-free programs enables many more people
+to use the whole GNU operating system, as well as its variant, the GNU/Linux operating system.
+
+Although the Lesser General Public License is Less protective of the users' freedom, it does ensure that the user of a
+program that is linked with the Library has the freedom and the wherewithal to run that program using a modified version
+of the Library.
+
+The precise terms and conditions for copying, distribution and modification follow. Pay close attention to the difference
+between a "work based on the library" and a "work that uses the library". The former contains code derived from the
+library, whereas the latter must be combined with the library in order to run.
+
+TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND
+MODIFICATION
+
+0. This License Agreement applies to any software library or other program which contains a notice placed by the
+copyright holder or other authorized party saying it may be distributed under the terms of this Lesser General Public
+License (also called "this License"). Each licensee is addressed as "you".
+
+A "library" means a collection of software functions and/or data prepared so as to be conveniently linked with application
+programs (which use some of those functions and data) to form executables.
+
+The "Library", below, refers to any such software library or work which has been distributed under these terms. A "work
+based on the Library" means either the Library or any derivative work under copyright law: that is to say, a work
+containing the Library or a portion of it, either verbatim or with modifications and/or translated straightforwardly into
+another language. (Hereinafter, translation is included without limitation in the term "modification".)
+
+"Source code" for a work means the preferred form of the work for making modifications to it. For a library, complete
+source code means all the source code for all modules it contains, plus any associated interface definition files, plus the
+scripts used to control compilation and installation of the library.
+
+Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The
+act of running a program using the Library is not restricted, and output from such a program is covered only if its contents
+constitute a work based on the Library (independent of the use of the Library in a tool for writing it). Whether that is true
+depends on what the Library does and what the program that uses the Library does.
+
+1. You may copy and distribute verbatim copies of the Library's complete source code as you receive it, in any medium,
+provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of
+warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and distribute a copy of
+this License along with the Library.
+
+You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in
+exchange for a fee.
+
+2. You may modify your copy or copies of the Library or any portion of it, thus forming a work based on the Library, and
+copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these
+conditions:
+
+ a) The modified work must itself be a software library.
+ b) You must cause the files modified to carry prominent notices stating that you changed the files and the date of any
+ change.
+ c) You must cause the whole of the work to be licensed at no charge to all third parties under the terms of this
+ License.
+ d) If a facility in the modified Library refers to a function or a table of data to be supplied by an application program
+ that uses the facility, other than as an argument passed when the facility is invoked, then you must make a good faith
+ effort to ensure that, in the event an application does not supply such function or table, the facility still operates, and
+ performs whatever part of its purpose remains meaningful.
+
+ (For example, a function in a library to compute square roots has a purpose that is entirely well-defined independent
+ of the application. Therefore, Subsection 2d requires that any application-supplied function or table used by this
+ function must be optional: if the application does not supply it, the square root function must still compute square
+ roots.)
+
+ These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from
+ the Library, and can be reasonably considered independent and separate works in themselves, then this License, and
+ its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the
+ same sections as part of a whole which is a work based on the Library, the distribution of the whole must be on the
+ terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every
+ part regardless of who wrote it.
+
+ Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather,
+ the intent is to exercise the right to control the distribution of derivative or collective works based on the Library.
+
+ In addition, mere aggregation of another work not based on the Library with the Library (or with a work based on the
+ Library) on a volume of a storage or distribution medium does not bring the other work under the scope of this
+ License.
+
+3. You may opt to apply the terms of the ordinary GNU General Public License instead of this License to a given copy of
+the Library. To do this, you must alter all the notices that refer to this License, so that they refer to the ordinary GNU
+General Public License, version 2, instead of to this License. (If a newer version than version 2 of the ordinary GNU
+General Public License has appeared, then you can specify that version instead if you wish.) Do not make any other change
+in these notices.
+
+Once this change is made in a given copy, it is irreversible for that copy, so the ordinary GNU General Public License
+applies to all subsequent copies and derivative works made from that copy.
+
+This option is useful when you wish to copy part of the code of the Library into a program that is not a library.
+
+4. You may copy and distribute the Library (or a portion or derivative of it, under Section 2) in object code or executable
+form under the terms of Sections 1 and 2 above provided that you accompany it with the complete corresponding
+machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium
+customarily used for software interchange.
+
+If distribution of object code is made by offering access to copy from a designated place, then offering equivalent access to
+copy the source code from the same place satisfies the requirement to distribute the source code, even though third parties
+are not compelled to copy the source along with the object code.
+
+5. A program that contains no derivative of any portion of the Library, but is designed to work with the Library by being
+compiled or linked with it, is called a "work that uses the Library". Such a work, in isolation, is not a derivative work of the
+Library, and therefore falls outside the scope of this License.
+
+However, linking a "work that uses the Library" with the Library creates an executable that is a derivative of the Library
+(because it contains portions of the Library), rather than a "work that uses the library". The executable is therefore
+covered by this License. Section 6 states terms for distribution of such executables.
+
+When a "work that uses the Library" uses material from a header file that is part of the Library, the object code for the
+work may be a derivative work of the Library even though the source code is not. Whether this is true is especially
+significant if the work can be linked without the Library, or if the work is itself a library. The threshold for this to be true is
+not precisely defined by law.
+
+If such an object file uses only numerical parameters, data structure layouts and accessors, and small macros and small
+inline functions (ten lines or less in length), then the use of the object file is unrestricted, regardless of whether it is legally
+a derivative work. (Executables containing this object code plus portions of the Library will still fall under Section 6.)
+
+Otherwise, if the work is a derivative of the Library, you may distribute the object code for the work under the terms of
+Section 6. Any executables containing that work also fall under Section 6, whether or not they are linked directly with the
+Library itself.
+
+6. As an exception to the Sections above, you may also combine or link a "work that uses the Library" with the Library to
+produce a work containing portions of the Library, and distribute that work under terms of your choice, provided that the
+terms permit modification of the work for the customer's own use and reverse engineering for debugging such
+modifications.
+
+You must give prominent notice with each copy of the work that the Library is used in it and that the Library and its use
+are covered by this License. You must supply a copy of this License. If the work during execution displays copyright
+notices, you must include the copyright notice for the Library among them, as well as a reference directing the user to the
+copy of this License. Also, you must do one of these things:
+
+ a) Accompany the work with the complete corresponding machine-readable source code for the Library including
+ whatever changes were used in the work (which must be distributed under Sections 1 and 2 above); and, if the work is
+ an executable linked with the Library, with the complete machine-readable "work that uses the Library", as object
+ code and/or source code, so that the user can modify the Library and then relink to produce a modified executable
+ containing the modified Library. (It is understood that the user who changes the contents of definitions files in the
+ Library will not necessarily be able to recompile the application to use the modified definitions.)
+ b) Use a suitable shared library mechanism for linking with the Library. A suitable mechanism is one that (1) uses at
+ run time a copy of the library already present on the user's computer system, rather than copying library functions
+ into the executable, and (2) will operate properly with a modified version of the library, if the user installs one, as
+ long as the modified version is interface-compatible with the version that the work was made with.
+ c) Accompany the work with a written offer, valid for at least three years, to give the same user the materials
+ specified in Subsection 6a, above, for a charge no more than the cost of performing this distribution.
+ d) If distribution of the work is made by offering access to copy from a designated place, offer equivalent access to
+ copy the above specified materials from the same place.
+ e) Verify that the user has already received a copy of these materials or that you have already sent this user a copy.
+
+For an executable, the required form of the "work that uses the Library" must include any data and utility programs needed
+for reproducing the executable from it. However, as a special exception, the materials to be distributed need not include
+anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and
+so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.
+
+It may happen that this requirement contradicts the license restrictions of other proprietary libraries that do not normally
+accompany the operating system. Such a contradiction means you cannot use both them and the Library together in an
+executable that you distribute.
+
+7. You may place library facilities that are a work based on the Library side-by-side in a single library together with other
+library facilities not covered by this License, and distribute such a combined library, provided that the separate distribution
+of the work based on the Library and of the other library facilities is otherwise permitted, and provided that you do these
+two things:
+
+ a) Accompany the combined library with a copy of the same work based on the Library, uncombined with any other
+ library facilities. This must be distributed under the terms of the Sections above.
+ b) Give prominent notice with the combined library of the fact that part of it is a work based on the Library, and
+ explaining where to find the accompanying uncombined form of the same work.
+
+8. You may not copy, modify, sublicense, link with, or distribute the Library except as expressly provided under this
+License. Any attempt otherwise to copy, modify, sublicense, link with, or distribute the Library is void, and will
+automatically terminate your rights under this License. However, parties who have received copies, or rights, from you
+under this License will not have their licenses terminated so long as such parties remain in full compliance.
+
+9. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to
+modify or distribute the Library or its derivative works. These actions are prohibited by law if you do not accept this
+License. Therefore, by modifying or distributing the Library (or any work based on the Library), you indicate your
+acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Library or
+works based on it.
+
+10. Each time you redistribute the Library (or any work based on the Library), the recipient automatically receives a
+license from the original licensor to copy, distribute, link with or modify the Library subject to these terms and conditions.
+You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not
+responsible for enforcing compliance by third parties with this License.
+
+11. If, as a consequence of a court judgment or allegation of patent infringement or for any other reason (not limited to
+patent issues), conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the
+conditions of this License, they do not excuse you from the conditions of this License. If you cannot distribute so as to
+satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you
+may not distribute the Library at all. For example, if a patent license would not permit royalty-free redistribution of the
+Library by all those who receive copies directly or indirectly through you, then the only way you could satisfy both it and
+this License would be to refrain entirely from distribution of the Library.
+
+If any portion of this section is held invalid or unenforceable under any particular circumstance, the balance of the section
+is intended to apply, and the section as a whole is intended to apply in other circumstances.
+
+It is not the purpose of this section to induce you to infringe any patents or other property right claims or to contest
+validity of any such claims; this section has the sole purpose of protecting the integrity of the free software distribution
+system which is implemented by public license practices. Many people have made generous contributions to the wide range
+of software distributed through that system in reliance on consistent application of that system; it is up to the author/donor
+to decide if he or she is willing to distribute software through any other system and a licensee cannot impose that choice.
+
+This section is intended to make thoroughly clear what is believed to be a consequence of the rest of this License.
+
+12. If the distribution and/or use of the Library is restricted in certain countries either by patents or by copyrighted
+interfaces, the original copyright holder who places the Library under this License may add an explicit geographical
+distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus
+excluded. In such case, this License incorporates the limitation as if written in the body of this License.
+
+13. The Free Software Foundation may publish revised and/or new versions of the Lesser General Public License from
+time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new
+problems or concerns.
+
+Each version is given a distinguishing version number. If the Library specifies a version number of this License which
+applies to it and "any later version", you have the option of following the terms and conditions either of that version or of
+any later version published by the Free Software Foundation. If the Library does not specify a license version number, you
+may choose any version ever published by the Free Software Foundation.
+
+14. If you wish to incorporate parts of the Library into other free programs whose distribution conditions are incompatible
+with these, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation,
+write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two
+goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software
+generally.
+
+NO WARRANTY
+
+15. BECAUSE THE LIBRARY IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE
+LIBRARY, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN
+WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE LIBRARY "AS IS" WITHOUT
+WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE
+ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE LIBRARY IS WITH YOU. SHOULD THE
+LIBRARY PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
+CORRECTION.
+
+16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY
+COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE LIBRARY
+AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL,
+INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE
+OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE LIBRARY TO OPERATE WITH
+ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+END OF TERMS AND CONDITIONS
\ No newline at end of file
diff --git a/doc/LICENSING b/doc/LICENSING
new file mode 100644
index 0000000..2fac434
--- /dev/null
+++ b/doc/LICENSING
@@ -0,0 +1,39 @@
+This software is free software and you may distribute it under the
+terms of the Library Gnu Public License (LGPL). Additionally several
+other external libraries are included and these are distributed under
+several other licenses.
+
+
+
+Currently these may include
+
+jakarta-regexp ASL
+xerces ASL
+java-getopts LGPL
+
+
+In accordance with the requirements of the ASL we state that
+
+"This product includes software developed by the
+Apache Software Foundation (http://www.apache.org/)."
+
+
+
+
+
+
+Copyright (C) 2001 For Authors see "AUTHORS" file
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
\ No newline at end of file
diff --git a/doc/cinema-changes.html b/doc/cinema-changes.html
new file mode 100644
index 0000000..37cbfca
--- /dev/null
+++ b/doc/cinema-changes.html
@@ -0,0 +1,454 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+
+<html>
+ <head>
+ <title>Cinema Changes</title>
+ </head>
+
+ <body>
+ <h1>Cinema Changes</h1>
+
+ <a name = "contents"></a>
+ <h2>Contents</h2>
+ <ul
+ <li><a href = "#release-3_0_23">Release 3.0.23</a></li>
+ <li><a href = "#release-3_0_22">Release 3.0.22</a></li>
+ <li><a href = "#release-3_0_21">Release 3.0.21</a></li>
+ <li><a href = "#release-3_0_20">Release 3.0.20</a></li>
+ <li><a href = "#release-3_0_19">Release 3.0.19</a></li>
+ <li><a href = "#release-3_0_18">Release 3.0.18</a></li>
+ <li><a href = "#release-3_0_17">Release 3.0.17</a></li>
+ <li><a href = "#release-3_0_16">Release 3.0.16</a></li>
+ <li><a href = "#release-3_0_16">Release 3.0.16</a></li>
+ <li><a href = "#release-3_0_15">Release 3.0.15</a></li>
+ <li><a href = "#release-3_0_14">Release 3.0.14</a></li>
+ <li><a href = "#release-3_0_13">Release 3.0.13</a></li>
+ <li><a href = "#release-3_0_12">Release 3.0.12</a></li>
+ <li><a href = "#release-3_0_11">Release 3.0.11</a></li>
+ <li><a href = "#release-3_0_10">Release 3.0.10</a></li>
+ <li><a href = "#release-3_0_9">Release 3.0.9</a></li>
+ <li><a href = "#release-3_0_8">Release 3.0.8</a></li>
+ <li><a href = "#release-3_0_7">Release 3.0.7</a></li>
+ <li><a href = "#release-3_0_6">Release 3.0.6</a></li>
+ <li><a href = "#release-3_0_5">Release 3.0.5</a></li>
+ <li><a href = "#release-3_0_4">Release 3.0.4</a></li>
+ </ul>
+
+ <a name = "Release-"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ Input error handling has been improved
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_22"></a>
+ <h2>Release</h2>
+
+ <h3>Bug fixes</h3>
+
+ <p>Fixed classpath</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_21"></a>
+
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ Manifest support in build file.
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_20"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>The launch script now takes sequence files on the command
+ line.
+ <li>Some new documentation has been added.
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>Minor changes to the build process</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_19"></a>
+ <h2>Release 3.0.19</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Motif default extensions fixed on saving</li>
+ <li>Multiple consensus viewer fixed</li>
+ </ul>
+
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3.0.18"></a>
+ <h2>Release 3.0.18</h2>
+
+ This release should be the last one before we move toward Cinema
+ 3.1, and should be considered to be a "release
+ candidate".
+
+ <h3>User Visible Changes</h3>
+ A few small usability changes, and some additions!
+ <ul>
+ <li>Lots of colour schemes added. Also color-convert.el for
+ people who want to import more colour schemes.</li>
+ <li>Moved some of the menu items around.</li>
+ <li>Home directory is now selected by default for motif
+ save</li>
+ <li>Resize keep square is default</li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+ <ul>
+ <li>Stack trace dumping when gaps are removed from groups no
+ longer occurs</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_17"></a>
+ <h2>Release 3.0.17</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Now updates display correctly when consensus calculator is
+ changed.</li>
+ <li>Regular expression search now works correctly</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_16"></a>
+ <h2>Release 3.0.16</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>main.xml is no longer required</li>
+ <li>Error handling for options much improved</li>
+ </ul>
+
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_15"></a>
+ <h2>Release 3.0.15</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Renamed menu items</li>
+ </ul>
+
+ <h3>Code changes</h3>
+ <ul>
+ <li>Consensus and colour map factories now support a default
+ option.</li>
+ <li>Removed spam debug messages</li>
+ <li>Default file input parser now configurable</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_14"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Fixed bug in launch script which was totally preventing it
+ from working!</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_13"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>A large number of changes to the build process</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3.0.12"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Updated version information correctly.
+ </li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3.0.11"></a>
+ <h2>Release-3.0.11</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>Changed build procedure, and directory structure associated
+ with it.</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_10"></a>
+ <h2>Release-3.0.10</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Now as well as being to search for regexp's
+ there is a menu item which should enable you to actually
+ search for regexps</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3.0.9"></a>
+ <h2>Release-3.0.9</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Cinema now remembers some details, such as window size,
+ element size and so on between different invocations</li>
+ <li>You can now search through sequences via regexp. The
+ interface is a little primitive at the moment, but will
+ improve. </li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+ <ul>
+ <li>Have now written ant scripts to build and install cinema</li>
+ <li>Installed persistance system</li>
+ <li>Altered module interface definition loading</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_8"></a>
+ <h2>Release-3.0.8</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>More status information is now printed out</li>
+ <li>Can now choose format on motif save</li>
+ <li>Can save only a single motif, as well as all of them</li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Fixed bug in PIR parser. Now writes 80 characters per line,
+ and no longer misses the last line</li>
+ <li>Enhancements to the XML loading process exception handling,
+ so problems are now a lot more informative</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>Can now configure a single module from several different places</li>
+ <li>Can now load configuration from .cinema/config directory</li>
+ <li>Have completely re-organised the XML loading</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_7"></a>
+ <h2>Release-3.0.7</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Motifs are now automatically sorted in the MotifManager
+ dialog. This also impacts on the saved name.
+ </li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>A repaint bug has been fixed so that AlignmentSelections can
+ be seen to grow smaller.</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "release-3.0.6"></a>
+ <h2>Release-3.0.6</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>This time I have definiately removed all references to
+ treedraw!</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "release-3_0_5"></a>
+ <h2>Release-3.0.5</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Removed references to treedraw which is not currently
+ checked in</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "release-3_0_4"></a>
+ <h2>Release 3.0.4</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Support for multiple selection</li>
+ <li>Initial version of Motif Manager added</li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ </body>
+</html>
+
+
+
+
+
\ No newline at end of file
diff --git a/doc/cinema-module/cinema-module.aux b/doc/cinema-module/cinema-module.aux
new file mode 100644
index 0000000..cefcd1f
--- /dev/null
+++ b/doc/cinema-module/cinema-module.aux
@@ -0,0 +1,51 @@
+\relax
+\newacro{Cinema-MX}{Colour INteractive Editor for Multiple Alignments}
+\newacro{MX}{Modular, eXtensible}
+\@writefile{toc}{\contentsline {section}{\numberline {1}Introduction}{1}}
+\@writefile{toc}{\contentsline {section}{\numberline {2}Requirements}{1}}
+\@writefile{toc}{\contentsline {section}{\numberline {3}Identifiers}{2}}
+\newlabel{lst:ident}{{1}{2}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {1}The ModuleIdentifier Interface}{2}}
+\newlabel{lst:enum}{{2}{2}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {2}The Abstract EnumeratedModuleIdentifier}{2}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Abstract Identifiers}{2}}
+\newlabel{sec:abstract-identifiers}{{3.1}{2}}
+\@writefile{toc}{\contentsline {section}{\numberline {4}The Module}{3}}
+\newlabel{sec:module-1}{{4}{3}}
+\newlabel{lst:module}{{3}{3}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {3}The Module class}{3}}
+\newlabel{lst:reqident}{{4}{3}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {4}An example of getRequiredIdentifiers}{3}}
+\newlabel{lst:reqmod}{{5}{3}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {5}An example of getRequiredModule}{3}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.1}Other methods}{4}}
+\newlabel{sec:other-methods}{{4.1}{4}}
+\@writefile{toc}{\contentsline {section}{\numberline {5}XML Loading and Configuration}{4}}
+\newlabel{sec:xml-load-conf}{{5}{4}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.1}Loading}{4}}
+\newlabel{sec:loading}{{5.1}{4}}
+\newlabel{lst:ident-dir}{{6}{4}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {6}The Identifier Directive}{4}}
+\newlabel{lst:mod-load}{{7}{5}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {7}Loading a Module}{5}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.2}Configuration}{5}}
+\newlabel{sec:configuration}{{5.2}{5}}
+\newlabel{lst:props}{{8}{5}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {8}Configuring Parsers}{5}}
+\newlabel{lst:trees}{{9}{5}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {9}Configuring the menu system}{5}}
+\gdef \LT at i {\LT at entry
+ {1}{115.50105pt}\LT at entry
+ {1}{253.49895pt}}
+\newlabel{lst:config}{{10}{6}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {10}The XML methods}{6}}
+\@writefile{toc}{\contentsline {section}{\numberline {6}Cinema-MX\xspace Modules}{6}}
+\newlabel{sec:cinema-modules}{{6}{6}}
+\newlabel{lst:cin-mod}{{11}{6}}
+\@writefile{lol}{\contentsline {lstlisting}{\numberline {11}The Cinema Module}{6}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {6.1}Cinema-MX\xspace modules in use}{6}}
+\newlabel{sec:cinema-modules-use}{{6.1}{6}}
+\@writefile{toc}{\contentsline {section}{\numberline {7}Step by Step}{6}}
+\newlabel{sec:step-step}{{7}{6}}
+\newlabel{tab:modules}{{6.1}{7}}
+\@writefile{lot}{\contentsline {table}{\numberline {2}{\ignorespaces The modules in use within the Cinema-MX\xspace application. The modules are organized by their super class, either the {\ttfamily \relax \fontsize {9}{11}\selectfont \abovedisplayskip 8.5\p@ plus3\p@ minus4\p@ \abovedisplayshortskip \z@ plus2\p@ \belowdisplayshortskip 4\p@ plus2\p@ minus2\p@ \def \leftmargin \leftmargini \parsep 4\p@ plus2\p@ minus\p@ \topsep 8\p@ plus2\p@ minus4\p@ \itemsep 4\p@ plus2\p@ minus\p@ { [...]
diff --git a/doc/cinema-module/cinema-module.dvi b/doc/cinema-module/cinema-module.dvi
new file mode 100644
index 0000000..7b9d1e3
Binary files /dev/null and b/doc/cinema-module/cinema-module.dvi differ
diff --git a/doc/cinema-module/cinema-module.log b/doc/cinema-module/cinema-module.log
new file mode 100644
index 0000000..69cb8e1
--- /dev/null
+++ b/doc/cinema-module/cinema-module.log
@@ -0,0 +1,244 @@
+This is TeX, Version 3.14159 (Web2C 7.3.1) (format=latex 2001.12.12) 20 APR 2002 15:49
+**\nonstopmode\input{cinema-module.tex}
+(cinema-module.tex (/usr/share/texmf/tex/latex/base/article.cls
+Document Class: article 2000/05/19 v1.4b Standard LaTeX document class
+(/usr/share/texmf/tex/latex/base/size10.clo
+File: size10.clo 2000/05/19 v1.4b Standard LaTeX file (size option)
+)
+\c at part=\count79
+\c at section=\count80
+\c at subsection=\count81
+\c at subsubsection=\count82
+\c at paragraph=\count83
+\c at subparagraph=\count84
+\c at figure=\count85
+\c at table=\count86
+\abovecaptionskip=\skip41
+\belowcaptionskip=\skip42
+\bibindent=\dimen102
+)
+(/usr/share/texmf/tex/latex/psnfss/times.sty
+Package: times 2000/01/12 PSNFSS-v8.1 Times font as default roman (SPQR)
+)
+(/home/phillord/documents/tex/listings/listings.sty
+Package: listings 2002/04/01 1.0 (Carsten Heinz)
+
+(/usr/share/texmf/tex/latex/graphics/keyval.sty
+Package: keyval 1999/03/16 v1.13 key=value parser (DPC)
+\KV at toks@=\toks14
+)
+\lst at mode=\count87
+\lst at gtempboxa=\box26
+\lst at token=\toks15
+\lst at length=\count88
+\lst at currlwidth=\dimen103
+\lst at column=\count89
+\lst at pos=\count90
+\lst at lostspace=\dimen104
+\lst at width=\dimen105
+\lst at newlines=\count91
+\lst at lineno=\count92
+\c at lstlisting=\count93
+\lst at maxwidth=\dimen106
+
+(/home/phillord/documents/tex/listings/lstpatch.sty
+File: lstpatch.sty 2002/04/15 1.0b (Carsten Heinz)
+)
+(/home/phillord/documents/tex/listings/lstmisc.sty
+File: lstmisc.sty 2002/04/01 1.0 (Carsten Heinz)
+\c at lstnumber=\count94
+\lst at skipnumbers=\count95
+\lst at framebox=\box27
+)
+(/home/phillord/documents/tex/listings/listings.cfg
+File: listings.cfg 2002/04/01 v1.0 listings configuration
+))
+(/usr/share/texmf/tex/latex/misc/supertabular.sty
+Package: supertabular 1999/08/07 v4.1d the supertabular environment
+\c at tracingst=\count96
+\ST at wd=\dimen107
+\ST at rightskip=\skip43
+\ST at leftskip=\skip44
+\ST at parfillskip=\skip45
+\ST at pageleft=\dimen108
+\ST at headht=\dimen109
+\ST at tailht=\dimen110
+\ST at pagesofar=\dimen111
+\ST at pboxht=\dimen112
+\ST at lineht=\dimen113
+\ST at stretchht=\dimen114
+\ST at prevht=\dimen115
+\ST at toadd=\dimen116
+\ST at dimen=\dimen117
+\ST at pbox=\box28
+)
+(/usr/share/texmf/tex/latex/tools/longtable.sty
+Package: longtable 1998/05/13 v4.09 Multi-page Table package (DPC)
+\LTleft=\skip46
+\LTright=\skip47
+\LTpre=\skip48
+\LTpost=\skip49
+\LTchunksize=\count97
+\LTcapwidth=\dimen118
+\LT at head=\box29
+\LT at firsthead=\box30
+\LT at foot=\box31
+\LT at lastfoot=\box32
+\LT at cols=\count98
+\LT at rows=\count99
+\c at LT@tables=\count100
+\c at LT@chunks=\count101
+\LT at p@ftn=\toks16
+)
+(/usr/share/texmf/tex/latex/base/alltt.sty
+Package: alltt 1997/06/16 v2.0g defines alltt environment
+)
+(/usr/share/texmf/tex/latex/tools/xspace.sty
+Package: xspace 1997/10/13 v1.06 Space after command names (DPC)
+)
+(/usr/share/texmf/tex/latex/html/url.sty
+Package: url 1999/03/02 ver 1.4 Verb mode for urls, email addresses, and file
+ names
+)
+(/usr/share/texmf/tex/latex/misc/acronym.sty
+Package: acronym
+)
+(/home/phillord/documents/tex/listings/lstlang1.sty
+File: lstlang1 2002/04/15 v1.0a listings language file
+) (cinema-module.aux)
+\openout1 = `cinema-module.aux'.
+
+LaTeX Font Info: Checking defaults for OML/cmm/m/it on input line 32.
+LaTeX Font Info: ... okay on input line 32.
+LaTeX Font Info: Checking defaults for T1/cmr/m/n on input line 32.
+LaTeX Font Info: ... okay on input line 32.
+LaTeX Font Info: Checking defaults for OT1/cmr/m/n on input line 32.
+LaTeX Font Info: ... okay on input line 32.
+LaTeX Font Info: Checking defaults for OMS/cmsy/m/n on input line 32.
+LaTeX Font Info: ... okay on input line 32.
+LaTeX Font Info: Checking defaults for OMX/cmex/m/n on input line 32.
+LaTeX Font Info: ... okay on input line 32.
+LaTeX Font Info: Checking defaults for U/cmr/m/n on input line 32.
+LaTeX Font Info: ... okay on input line 32.
+LaTeX Font Info: Try loading font information for OT1+ptm on input line 32.
+
+(/usr/share/texmf/tex/latex/psnfss/ot1ptm.fd
+File: ot1ptm.fd 2000/01/12 PSNFSS-v8.1 font definitions for OT1/ptm.
+)
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <12> on input line 34.
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <8> on input line 34.
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <6> on input line 34.
+LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <9> not available
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 36.
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <9> on input line 37.
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <5> on input line 37.
+LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <14.4> not available
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 44.
+LaTeX Font Info: Try loading font information for OMS+ptm on input line 67.
+
+(/usr/share/texmf/tex/latex/psnfss/omsptm.fd
+File: omsptm.fd
+)
+LaTeX Font Info: Font shape `OMS/ptm/m/n' in size <10> not available
+(Font) Font shape `OMS/cmsy/m/n' tried instead on input line 67.
+ [1
+
+]
+LaTeX Font Info: Try loading font information for OT1+pcr on input line 88.
+
+(/usr/share/texmf/tex/latex/psnfss/ot1pcr.fd
+File: ot1pcr.fd 2000/01/12 PSNFSS-v8.1 font definitions for OT1/pcr.
+)
+LaTeX Font Info: Font shape `OT1/pcr/bx/n' in size <5> not available
+(Font) Font shape `OT1/pcr/b/n' tried instead on input line 89.
+LaTeX Font Info: Font shape `OT1/pcr/m/it' in size <5> not available
+(Font) Font shape `OT1/pcr/m/sl' tried instead on input line 94.
+
+Overfull \hbox (2.14824pt too wide) in paragraph at lines 97--101
+\OT1/pcr/m/n/9 lic String get-Mod-u-le-Name() \OT1/ptm/m/n/10 de-fine the link
+be-tween a mod-ule and a String which
+ []
+
+LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <12> not available
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 137.
+[2]
+Overfull \hbox (8.21921pt too wide) in paragraph at lines 199--203
+[]\OT1/ptm/m/n/10 The sec-ond method \OT1/pcr/m/n/9 pub-lic Mod-ule ge-tRe-quir
+ed-Mod-ule(ModuleIdentifier
+ []
+
+
+Overfull \hbox (9.67682pt too wide) in paragraph at lines 212--221
+[]\OT1/ptm/m/n/10 The meth-ods deal-ing with mod-ule func-tion-al-ity are hope-
+fully largely self-explanatory.
+ []
+
+[3] (/home/phillord/documents/tex/listings/lstlang1.sty
+File: lstlang1 2002/04/15 v1.0a listings language file
+)
+(/home/phillord/documents/tex/listings/lstmisc.sty
+File: lstmisc.sty 2002/04/01 1.0 (Carsten Heinz)
+) [4] [5]
+LaTeX Font Info: External font `cmex10' loaded for size
+(Font) <7> on input line 387.
+
+Underfull \hbox (badness 10000) in paragraph at lines 444--444
+[]|\OT1/ptm/m/n/10 CinemaCommand-
+ []
+
+
+Underfull \hbox (badness 10000) in paragraph at lines 452--452
+[]|\OT1/ptm/m/n/10 CinemaMultiple-
+ []
+
+
+Overfull \hbox (9.1678pt too wide) in paragraph at lines 458--458
+[]|\OT1/ptm/m/n/10 CinemaSlaveViewerModule|
+ []
+
+LaTeX Font Info: Font shape `OT1/ptm/bx/n' in size <10> not available
+(Font) Font shape `OT1/ptm/b/n' tried instead on input line 462.
+
+Underfull \hbox (badness 10000) in paragraph at lines 472--472
+[]|\OT1/ptm/m/n/10 CinemaConsensus-
+ []
+
+
+Overfull \hbox (24.0pt too wide) in alignment at lines 439--472
+ [] []
+ []
+
+
+Underfull \vbox (badness 10000) detected at line 472
+ []
+
+
+Overfull \hbox (24.0pt too wide) in alignment at lines 472--497
+ [] []
+ []
+
+
+LaTeX Warning: Float too large for page by 0.22955pt on input line 503.
+
+[6] [7]
+Overfull \hbox (6.98935pt too wide) in paragraph at lines 515--522
+\OT1/pcr/m/n/9 man . bioinf . apps . cinema . utils . CinemaSlaveViewerModule$\
+OT1/ptm/m/n/10 . This mod-
+ []
+
+[8] (cinema-module.aux) )
+Here is how much of TeX's memory you used:
+ 2012 strings out of 20887
+ 26393 string characters out of 196273
+ 95631 words of memory out of 350001
+ 4971 multiletter control sequences out of 10000+15000
+ 15303 words of font info for 45 fonts, out of 400000 for 1000
+ 14 hyphenation exceptions out of 10000
+ 28i,8n,61p,1681b,723s stack positions out of 3000i,100n,1500p,50000b,4000s
+
+Output written on cinema-module.dvi (8 pages, 41152 bytes).
diff --git a/doc/cinema-module/cinema-module.pdf b/doc/cinema-module/cinema-module.pdf
new file mode 100644
index 0000000..cb7aebf
Binary files /dev/null and b/doc/cinema-module/cinema-module.pdf differ
diff --git a/doc/cinema-module/cinema-module.tex b/doc/cinema-module/cinema-module.tex
new file mode 100644
index 0000000..c83abe2
--- /dev/null
+++ b/doc/cinema-module/cinema-module.tex
@@ -0,0 +1,540 @@
+
+
+\documentclass[10pt, a4paper]{article}
+
+\usepackage{times}
+\usepackage{listings}
+\usepackage{supertabular}
+\usepackage{longtable}
+\usepackage{alltt}
+\usepackage{xspace}
+\usepackage{url}
+\usepackage[footnote]{acronym}
+
+\newcommand{\Cinema}
+{\ac{Cinema-MX}\xspace}
+\newcommand{\MX}
+{\ac{MX}\xspace}
+
+\acrodef{Cinema-MX}{Colour INteractive Editor for Multiple Alignments}
+\acrodef{MX}{Modular, eXtensible}
+
+\newcommand{\code}[1]{{\ttfamily\small#1}}
+
+
+\title{The \acs{MX} architecture and its usage within
+ the \acs{Cinema-MX} application}
+\lstset{language=Java, float,
+ captionpos=b, frame=tblr, basicstyle=\ttfamily\tiny}
+
+\author{Phillip Lord}
+
+\begin{document}
+
+\maketitle
+
+\begin{abstract}
+ This document describes the \MX architecture, and how it has been
+ used in the \Cinema application. Its meant both as an overview of
+ the architecture, and also a introduction for those who might wish
+ to develop new modules for the application.
+\end{abstract}
+
+
+\section{Introduction}
+
+The \MX architecture was designed to allow \Cinema (or other
+applications) to be extended straightforwardly and simply. This is
+achieved by splitting the application up into a series of small
+modules. These modules can then be put together to form the end
+application.
+
+For the \Cinema application as well as allowing modularity we wanted
+to gain extensibility, allowing the user to integrate new modules into
+\Cinema, without requiring alteration of the main code base. To this
+end, XML has been used to define which modules should be loaded, and
+also to provide some configuration for these modules if required.
+
+In the following documentation I describe how the \MX architecture
+works and what all the various bits do. If you can't be bothered to
+read this, then there is a very quick ``step-by-step'' guide in
+Section~\ref{sec:step-step}, which you might prefer.
+
+\section{Requirements}
+
+There were a number of requirements for the \MX architecture.
+\begin{itemize}
+\item The architecture should be relatively \emph{light-weight}. That
+ is it should be verbose, which would discourage programmers from
+ making small modules.
+\item The basic architecture should be as customisable as possible.
+\item The architecture should be \emph{fail fast}, that is it should
+ break early, rather than run incorrectly.
+\item Dependency between modules should be explicit.
+\item Loading should be as rapid as possible.
+\end{itemize}
+
+\section{Identifiers}
+
+The requirement that module dependency should be explicit creates a
+problem. One module must be able to refer to another. However if that
+class is referred to directly, then the class will be loaded
+immediately, when we might want to defer it.
+
+To circumvent this problem, we use an identifier class, which can be
+used to refer to the module, the interface for this is shown in
+Listing \ref{lst:ident}.
+
+\begin{lstlisting}[label=lst:ident, caption=The ModuleIdentifier Interface]{}
+public interface ModuleIdentifier
+{
+ public boolean isInterface();
+ public String getClassName();
+ public String getModuleName();
+}// ModuleIdentifier
+\end{lstlisting}
+
+The two methods in this interface \code{public String getClassName()}
+and \code{public String getModuleName()} define the link between a
+module and a String which can be used to refer to it, which solves the
+problem of referring to a Module (by a name) and a Class.
+
+One difficulty with this is that using a String (the module name) to
+refer to a module is not type safe, and will result in errors when the
+name is typed incorrectly. This difficulty is solved by extending the
+class \code{AbstractEnumeratedModuleIdentifier}. This uses the a
+variation of the theme of the Singleton design pattern to create an
+identifier class which is relatively type safe. An example of its
+usage from \Cinema is shown in Listing \ref{lst:enum}. This class uses
+reflection to translate the variable name of its instances, into the
+String that it uses for its Module name.
+
+
+\begin{lstlisting}[label=lst:enum, caption=The Abstract EnumeratedModuleIdentifier]{}
+public class CinemaBootIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+ private CinemaBootIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+ public static final CinemaBootIdentifier CINEMA_BOOT =
+ new CinemaBootIdentifier( "uk.ac.man.bioinf.apps.cinema.CinemaBoot",
+ "Main Cinema Boot Class" );
+ public static final CinemaBootIdentifier CINEMA_SHARED =
+ new CinemaBootIdentifier( "uk.ac.man.bioinf.apps.cinema.CinemaShared",
+ "Shared Boot Class" );
+} // CinemaBootIdentifier
+\end{lstlisting}
+
+The practical upshot of all of this is that to refer to for instance
+the main Cinema Boot Module, the CINEMA\_BOOT instance can be used
+directly. Its still possible to type this incorrectly of course, but
+this will be detected at compile time. Its also possible to type the
+class name incorrectly when writing the identifier, but at least this
+needs to only be done once.
+
+
+\subsection{Abstract Identifiers}
+\label{sec:abstract-identifiers}
+
+There is a final method in the \code{ModuleIdentifier} class, called
+\code{isInteface}. Normally this will return false, but it is possible
+to define a module which acts like an abstract class, and delegates
+its functionality to another module. This allows a degree of
+polymorphism for modules. This feature is not used very widely within
+\Cinema, as it turned out to be less needed than it appeared to be
+during design. For most purposes its easier to use ``Optional
+Modules'' which are described in Section \ref{sec:module-1}.
+
+\section{The Module}
+\label{sec:module-1}
+
+The \code{ModuleIdentifier}interface refers to a Class name. This
+Class should be a instance of the \code{Module} class. Its interface
+is shown in Listing \ref{lst:module}. There are quite a few other
+methods in this class, but most of them have been elided here for the
+sake of simplicity.
+
+\begin{lstlisting}[label=lst:module,caption=The Module class]{}
+public abstract class Module
+{
+ public void load() throws ModuleException {};
+ public void start();
+ public void destroy();
+ public ModuleIdentifierList getRequiredIdentifiers();
+ public Module getRequiredModule( ModuleIdentifier ident );
+ public abstract String getVersion();
+} // Module
+\end{lstlisting}
+
+
+We can divide the methods shown here into three groups.
+\begin{itemize}
+\item Those related to dependency with other modules.
+\item Those directly to do with the function of the Module.
+\item And the other method.
+\end{itemize}
+
+Dealing with this in order. One of the requirements is for explicit
+dependency between modules. This is provided by the
+\code{public ModuleIdentifierList getRequiredIdentifiers()} method. In
+this method any modules which this module depends on should be
+identified. For example, see Listing \ref{lst:reqident}, which comes
+from the \code{CinemaConsensusDisplay} module. This requires two other
+modules, namely \code{CinemaConsensus}, which actually takes on the
+task of calculating the consensus, and \code{CinemaSystemEvents}. The
+consensus display is threaded, and needs to know when the application
+is about to close, so that it can shut down cleanly.
+
+\begin{lstlisting}[label=lst:reqident, caption=An example of getRequiredIdentifiers]{}
+public ModuleIdentifierList getRequiredIdentifiers()
+{
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaConsensusIdentifier.CINEMA_CONSENSUS );
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+}
+\end{lstlisting}
+
+The second method \code{public Module
+getRequiredModule(ModuleIdentifier ident)} actually allows access to
+these modules. Listing \ref{lst:reqmod} comes again from the
+\code{CinemaConsensusDisplay} class
+
+\begin{lstlisting}[label=lst:reqmod, caption=An example of getRequiredModule]{}
+if( queue == null ){
+ queue = new InvokerInternalQueue
+ ( (CinemaSystemEvents)getRequiredModule
+ ( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS ) );
+}
+\end{lstlisting}
+
+The methods dealing with module functionality are hopefully largely
+self-explanatory. When the module is initially loaded, unsurprising
+the \code{public void load{}} method is called. During this time the
+module should perform any initialisation that is required. The rule at
+this time is that only initialisation that does not require other
+modules should be performed, as this may well not be available yet. Or
+in another way, while the \code{load()} method is running, there are
+no guarantee's about what the \code{getRequiredModule()} method will
+return (most likely it will return \code{null}).
+
+Immediately after this time the \code{public void start()} method will
+be called. At this time it is guaranteed that the
+\code{getRequiredModule()} method will return any of the Modules
+identified, and that further all of their \code{load()} methods will
+have been called and have successfully completed.
+
+This is actually simpler than it sounds, but it's designed to cope
+with a fairly complex dependency graph, and generally it just
+works. No checking is performed to ensure that the graph is acyclic
+The system will crash if you do this, but as per the design
+requirement it will fail immediately.
+
+And finally the other method. This is meant to return a String
+identifying the version of the Module. This is not widely used. No
+specific semantics is required for this String, and generally the CVS
+version keyword has been used. This might be removed at a later date.
+
+
+\subsection{Other methods}
+\label{sec:other-methods}
+
+There are a few other methods which are potentially of interest within
+the \code{Module} interface. Firstly the \code{Module} provides access
+to the \code{ModuleContext} class, which contains the \code{public
+Module getModule(ModuleIdentifier ident)}. This enables access to
+any other Modules in the system, beyond those named as required
+modules. As they are not required they may be unavailable, so checking
+the \code{ public boolean isModuleAvailable(ModuleIdentifier
+identifier)} first is probably wise.
+
+And finally the \code{ModuleContext} class gives access to the
+\code{public Object getConfig()} method. Of itself this is not that
+useful. Its used internally to provide XML configuration though, which
+is described in Section~\ref{sec:configuration}.
+
+\section{XML Loading and Configuration}
+\label{sec:xml-load-conf}
+
+The module system described so far provides a basic
+architecture. However some mechanism needs to be available to define
+which modules should be used. While it is possible to do this using
+Java directly this would require the user to possess a Java compiler
+to enable new modules, or reconfigure existing ones. By defining the
+loading and configuration in XML, it's possible to do this using a
+text editor.
+
+
+\subsection{Loading}
+\label{sec:loading}
+
+As described in Section \ref{sec:abstract-identifiers}, each module
+referred to by a \code{ModuleIdentifier}. In order to load first the
+ModuleIdentifier must be made available to the system.
+The \code{Identifier} directive can be used to this end, as shown in
+Listing \ref{lst:ident-dir}. This code assumes that the
+\code{AbstractEnumeratedModuleIdentifier} has been used. For further
+information see the \code{module.dtd} file in the source, which is
+heavily documented. Its worth remembering that the
+\code{AbstractEnumeratedModuleIdentifier} can contain identifiers for
+many different modules, so relatively few of these statements are
+needed. In \Cinema the modules are grouped into functional units. The
+overhead of loading an \code{ModuleIdentifier} is very low (a few objects
+for each additional one), so there is not really any problem in
+loading these, even if the module is not used in the end.
+
+\begin{lstlisting}[language=HTML, caption=The Identifier Directive, label=lst:ident-dir]{}
+<identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier</class>
+ </enumeration>
+</identifier>
+\end{lstlisting}
+
+Having made the \code{ModuleIdentifier} available, the module itself
+can be loaded or started from within the XML, using the \code{load}
+and \code{start} directive. The module is referred to by the name
+returned by the identifier. For example, the code
+in~\ref{lst:mod-load} shows loading and starting of the module that
+provides the ``status bar'' in \Cinema.
+
+\begin{lstlisting}[language=HTML, caption=Loading a Module, label=lst:mod-load]{}
+<load>
+ <name>CINEMA_STATUS</name>
+</load>
+<start>
+ <name>CINEMA_STATUS</name>
+</start>
+\end{lstlisting}
+
+
+\subsection{Configuration}
+\label{sec:configuration}
+
+As well as loading modules its also possible to configure them. At the
+current time, the configuration can come in one of two forms, which
+are a properties list, or a tree structure. For example in
+Listing~\ref{lst:props} the configuration which is used for input
+module, is shown. It defines ``parsers'' which are used to output
+sequence data. This configurability means that it's to possible to add
+new ``parsers'' (perhaps inappropriately named as they are used for
+both input and output of sequences) \Cinema, by altering the
+configuration for this module.
+
+\begin{lstlisting}[label=lst:props, caption=Configuring Parsers]{}
+<properties>
+ <paramname>PIR</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser</value>
+ </param>
+ <param>
+ <paramname>MOT</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.MotProteinParser</value>
+ </param>
+</properties>
+\end{lstlisting}
+
+The second type of configuration is a simple tree structure, which
+can be seen in Listing~\ref{lst:trees}. In this case the menu system
+is being configured. In this case most of the configuration has been
+elided. Generally speaking the properties configuration is to be
+preferred because its much simpler, but the tree structure is much
+more versatile, and means that tricks, such as providing additional
+semantics to the keys of the properties lists are not necessary.
+
+\begin{lstlisting}[language=HTML, caption=Configuring the menu system, label=lst:trees]{}
+<tree>
+ <!-- The File Menu -->
+ <node>
+ <value>File</value>
+ <node>
+ <!-- Provides the open alignment -->
+ <name>SEQ_INPUT</name>
+ </node>
+ <node>
+ <!-- Provides the save alignment -->
+ <name>SEQ_OUTPUT</name>
+ </node>
+ <node>
+ <!-- Provides the exit menu -->
+ <name>CINEMA_CORE_GUI</name>
+ </node>
+ </node>
+</tree>
+\end{lstlisting}
+
+In order for the modules to access this configuration two methods (see
+Listing~\ref{lst:config}) are provided by the \code{XMLModule} class
+which all the \Cinema modules extend from. The standard Java
+\code{Properties} class has been used here. Sadly Java does not
+provide a standard Tree class, so a simple one has been provided.
+
+\begin{lstlisting}[label=lst:config, caption=The XML methods]{}
+public Properties getConfigProperties();
+public ConfigNode getConfigTree();
+\end{lstlisting}
+
+\section{\Cinema Modules}
+\label{sec:cinema-modules}
+
+Although the \MX architecture provides the ability to define modules,
+and their interaction with each other, they do not provide any
+specific Cinema functionality. It would be possible to provide all of
+this functionality through the \MX system, by accessing specific
+modules. However for convenience the \code{XMLModule} class has been
+extended, to give access to a number of different method, through the
+\code{CinemaModule} class.
+\footnote{As it happens, this has been implemented by accessing
+ modules through the \MX architecture. All of the functionality
+ provide by the \code{CinemaModule} is actually delegated to a
+ \code{XMLModule} called \code{CinemaCoreView}, while all of the
+ functionality provide by the more specific \code{CinemaGuiModule} is
+ serviced by the \code{CinemaCoreGui} module.}
+Additionally there is a more specific \code{CinemaCoreGui} class,
+which gives access to more methods, which gives direct access to the
+widgets used to build the basic \Cinema frame. Essentially the rule is
+extend the \code{CinemaModule} unless you really need the
+\code{CinemaGuiModule} as the latter is less likely to remain stable.
+
+
+\begin{lstlisting}[caption=The Cinema Module, label=lst:cin-mod]{}
+public abstract class CinemaModule extends XMLModule
+ implements AlignmentEventProvider
+{
+ public SequenceAlignment getSequenceAlignment()
+ public void setSequenceAlignment( SequenceAlignment seq )
+ public ColorMap getColorMap()
+ public void setColorMap( ColorMap map )
+ public AlignmentSelectionModel getAlignmentSelectionModel()
+ public void setAlignmentSelectionModel( AlignmentSelectionModel model )
+ public void setSequenceTitleColor( GappedSequence seq, Color colour )
+ public void clearSequenceTitleColor( GappedSequence seq )
+ public void sendStatusMessage( String message )
+} // CinemaModule
+\end{lstlisting}
+
+The interface of the \code{CinemaModule} is shown in
+Listing~\ref{lst:cin-mod}. Direct access is provided to the alignment
+being shown, to the \code{ColorMap}.
+\footnote{In the interests of international co-operation, it should be
+ noted that the shorter spelling of the word ``Color'' was used. In
+ the interests of flag waving jingoism, it should be noted that it
+ hurt, it really hurt.}
+The other methods give access to other information associated with the
+view, including the Selection Model, the colour associated with the
+sequence, and a status message which appears at the bottom of the
+\Cinema frame.
+
+
+\subsection{\Cinema modules in use}
+\label{sec:cinema-modules-use}
+
+The \MX architecture works best if the individual \code{Module}'s are
+relatively small. To give some idea of how this works in \Cinema, the
+\code{Module}'s are described in Table~\ref{tab:modules}. Some of
+these are very small (100 lines or so), and some quite a bit larger,
+and use several other specialised classes.
+
+\begin{table}
+ \begin{longtable}{|p{0.3\textwidth}|p{0.7\textwidth}|}
+\hline\hline
+CinemaModule & Function \\ \hline \hline
+CinemaColorFactory & Generates \code{ColorMap} instances, and menu
+items for their selection.\\ \hline
+CinemaCommand\-LineParser & Parses the command line, and acts on it.\\ \hline
+CinemaConsensus & Provides calculation of consensus sequences \\
+\hline
+CinemaGroupModule & Group sequences, for editing, viewing, and
+analysis. \\ \hline
+CinemaMenuBuilder & Generate menu items on the basis of the XML
+configurations \\ \hline
+CinemaMotifModule & The MotifManager dialog, and output \\\hline
+CinemaMultiple\-ConsensusViewer & View consensus sequences of groups,
+and there variance. \\\hline
+CinemaPersist & Save information between instantiations of \Cinema
+\\\hline
+CinemaRegexp & Regular Expression searches down sequences \\\hline
+CinemaResizeElements & Resize sequence cells \\\hline
+CinemaSlaveViewerModule & Generate viewer frames for use by other
+modules.\\\hline
+CinemaSplash & Adds massive functionality in the form of a Splash
+screen. \\\hline
+FormGroupsByPrints & \textbf{Experimental!} Queries the PRINTS\_S
+database to display the PRINTS motifs. \\\hline
+PhylipInvoker & \textbf{Experimental!} Displays a phylogenetic
+tree. \\
+\hline\hline
+CinemaGuiModule & \\
+\hline\hline
+AbstractSequence\-Input & Input sequence by some route. \\\hline
+AbstractSequence\-Output & Output sequence by some route.\\\hline
+CinemaColorSelector & Select \code{ColorMap}. \\\hline
+CinemaConsensus\-Display & Displays the consensus sequences. \\\hline
+CinemaCoreView & Support for CinemaModule class \\\hline
+CinemaGo & Well everybody hacks some times \\\hline
+CinemaHackMenu & More professionally displayed as ``in development''
+in the menu system. Its quicker to add here than through XML. \\\hline
+CineamMenuSystem & Uses CinemaMenuBuilder to build menu, then displays
+it \\\hline
+CinemaSequenceMenu & Right click on sequence button menu. \\\hline
+CinemaStatusInformation & Prints ``cursor here'' information in status
+bar. \\
+\hline\hline
+Others & \\
+\hline\hline
+CinemaCoreGui & Extends directly from the \code{Module} class, and
+provides support for the CinemaGuiModule class. \\ \hline
+XMLBootModule & Extends from directly from \code{Module}. Loads1
+parsers for reading XML configuration. \\ \hline
+CinemaBoot & Extends from \code{XMLBootModule}. Additional support for
+\Cinema XML loading. \\\hline
+CinemaFile\-Persist & Extends from \code{CinemaPersist}. Save
+persistence data to file.\\\hline
+FileSequenceInput & Extends from \code{AbstractSequenceInput}.
+Load from file. \\\hline
+FileSequenceOutput & Extends from \code{AbstractSequenceOutput}.
+Save to file. \\\hline
+ \end{longtable}
+ \label{tab:modules}
+ \caption{The modules in use within the \Cinema application. The
+ modules are organized by their super class, either the
+ \code{CinemaModule}, the \code{CinemaGuiModule}, or
+ \code{Others}, which are extended from some other module. }
+\end{table}
+
+
+\section{Step by Step}
+\label{sec:step-step}
+
+\begin{enumerate}
+\item Define a new identifier class. See for instance
+ \code{\url{uk.ac.man.bioinf.apps.cinema.util.CinemaUtilityIdentifier}}.
+ Make sure that you get the class name of your module correct. I tend
+ to group my identifiers into logical blocks, as loading identifiers
+ for modules that you don't actually use, has a very low overhead.
+\item Define a new module class. This can be very small. Take for
+ instance \code{
+ \url{uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule}}. This
+ module is used only by other modules. The
+ \code{\url{uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation}} is
+ a ``user-facing'' module, that is also very simple. It provides the
+ ``cursor information'' in the status bar.
+\item Write, or add to a ``main.xml''. This file should be placed in
+ ``./cinema/config''. This directory should already exist if you have
+ run \Cinema. This is a simple XML file with a top level tag of
+ ``configuration''. The DTD can be found in the \Cinema source.
+\item Load your identifier code. Listing \ref{lst:ident-dir} shows how
+ to do this.
+\item Actually load and start the module. Listing \ref{lst:mod-load}
+ shows how to do this.
+\end{enumerate}
+
+And pretty much that should be it.
+
+\end{document}
+
+
+%%% Local Variables:
+%%% mode: latex
+%%% TeX-master: t
+%%% End:
diff --git a/doc/cinema-module/cinema-module.wiz b/doc/cinema-module/cinema-module.wiz
new file mode 100644
index 0000000..e69de29
diff --git a/doc/cinema-module/cinema-module/WARNINGS b/doc/cinema-module/cinema-module/WARNINGS
new file mode 100644
index 0000000..034459c
--- /dev/null
+++ b/doc/cinema-module/cinema-module/WARNINGS
@@ -0,0 +1,6 @@
+No implementation found for style `url'
+No implementation found for style `acronym'
+
+cinema-module.tex is newer than cinema-module.aux: Please rerun latex.
+
+No number for "ThemodulesinusewithintheCinema-MXapplication.Themodulesareorganizedbytheirsuperclass,eitherthe<TT><FONTSIZE="-1">CinemaModule</FONT></TT>,the<TT><FONTSIZE="-1">CinemaGuiModule</FONT></TT>,or<TT><FONTSIZE="-1">Others</FONT></TT>,whichareextendedfromsomeothermodule."
diff --git a/doc/cinema-module/cinema-module/cinema-module.css b/doc/cinema-module/cinema-module/cinema-module.css
new file mode 100644
index 0000000..aad8978
--- /dev/null
+++ b/doc/cinema-module/cinema-module/cinema-module.css
@@ -0,0 +1,30 @@
+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH { font-family: "Century Schoolbook", serif; }
+.MATH I { font-family: "Century Schoolbook", serif; font-shape: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
+SMALL.XTINY { font-size : xx-small }
+SMALL.TINY { font-size : x-small }
+SMALL.SCRIPTSIZE { font-size : smaller }
+SMALL.FOOTNOTESIZE { font-size : small }
+SMALL.SMALL { }
+BIG.LARGE { }
+BIG.XLARGE { font-size : large }
+BIG.XXLARGE { font-size : x-large }
+BIG.HUGE { font-size : larger }
+BIG.XHUGE { font-size : xx-large }
+
+/* heading styles */
+H1 { }
+H2 { }
+H3 { }
+H4 { }
+H5 { }
+
+/* mathematics styles */
+DIV.displaymath { } /* math displays */
+TD.eqno { } /* equation-number cells */
+
+
+/* document-specific styles come next */
diff --git a/doc/cinema-module/cinema-module/cinema-module.html b/doc/cinema-module/cinema-module/cinema-module.html
new file mode 100644
index 0000000..8c59c3b
--- /dev/null
+++ b/doc/cinema-module/cinema-module/cinema-module.html
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>The MX architecture and its usage within the Cinema-MX application</TITLE>
+<META NAME="description" CONTENT="The MX architecture and its usage within the Cinema-MX application">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html8"
+ HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up_g.png">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev_g.png">
+<BR>
+<B> Next:</B> <A NAME="tex2html9"
+ HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+<H1 ALIGN="CENTER">The MX architecture and its usage within
+ the Cinema-MX application</H1>
+<P ALIGN="CENTER"><STRONG>Phillip Lord</STRONG></P>
+
+<P>
+
+<H3>Abstract:</H3>
+<DIV>
+This document describes the MX architecture, and how it has been
+ used in the Cinema-MX application. Its meant both as an overview of
+ the architecture, and also a introduction for those who might wish
+ to develop new modules for the application.
+</DIV>
+<P>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html10"
+ HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html11"
+ HREF="node2.html">Requirements</A>
+<LI><A NAME="tex2html12"
+ HREF="node3.html">Identifiers</A>
+<UL>
+<LI><A NAME="tex2html13"
+ HREF="node4.html">Abstract Identifiers</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html14"
+ HREF="node5.html">The Module</A>
+<UL>
+<LI><A NAME="tex2html15"
+ HREF="node6.html">Other methods</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html16"
+ HREF="node7.html">XML Loading and Configuration</A>
+<UL>
+<LI><A NAME="tex2html17"
+ HREF="node8.html">Loading</A>
+<LI><A NAME="tex2html18"
+ HREF="node9.html">Configuration</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html19"
+ HREF="node10.html">Cinema-MX Modules</A>
+<UL>
+<LI><A NAME="tex2html20"
+ HREF="node11.html">Cinema-MX modules in use</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html21"
+ HREF="node12.html">Step by Step</A>
+<LI><A NAME="tex2html22"
+ HREF="node13.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/footnode.html b/doc/cinema-module/cinema-module/footnode.html
new file mode 100644
index 0000000..fe01208
--- /dev/null
+++ b/doc/cinema-module/cinema-module/footnode.html
@@ -0,0 +1,107 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Footnotes</TITLE>
+<META NAME="description" CONTENT="Footnotes">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="previous" HREF="node12.html">
+<LINK REL="up" HREF="cinema-module.html">
+</HEAD>
+
+<BODY >
+
+<DL>
+<DT><A NAME="foot197">... class.</A><A NAME="foot197"
+ HREF="node10.html#tex2html1"><SUP>1</SUP></A>
+<DD>As it happens, this has been implemented by accessing
+ modules through the MX architecture. All of the functionality
+ provide by the <TT><FONT SIZE="-1">CinemaModule</FONT></TT> is actually delegated to a
+ <TT><FONT SIZE="-1">XMLModule</FONT></TT> called <TT><FONT SIZE="-1">CinemaCoreView</FONT></TT>, while all of the
+ functionality provide by the more specific <TT><FONT SIZE="-1">CinemaGuiModule</FONT></TT> is
+ serviced by the <TT><FONT SIZE="-1">CinemaCoreGui</FONT></TT> module.
+<PRE>.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+</PRE>
+<DT><A NAME="foot154">... SIZE="-1">ColorMap</FONT></TT>.</A><A NAME="foot154"
+ HREF="node10.html#tex2html2"><SUP>2</SUP></A>
+<DD>In the interests of international co-operation, it should be
+ noted that the shorter spelling of the word ``Color'' was used. In
+ the interests of flag waving jingoism, it should be noted that it
+ hurt, it really hurt.
+<PRE>.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+.
+</PRE>
+</DL>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/index.html b/doc/cinema-module/cinema-module/index.html
new file mode 100644
index 0000000..8c59c3b
--- /dev/null
+++ b/doc/cinema-module/cinema-module/index.html
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>The MX architecture and its usage within the Cinema-MX application</TITLE>
+<META NAME="description" CONTENT="The MX architecture and its usage within the Cinema-MX application">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html8"
+ HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up_g.png">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev_g.png">
+<BR>
+<B> Next:</B> <A NAME="tex2html9"
+ HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+<H1 ALIGN="CENTER">The MX architecture and its usage within
+ the Cinema-MX application</H1>
+<P ALIGN="CENTER"><STRONG>Phillip Lord</STRONG></P>
+
+<P>
+
+<H3>Abstract:</H3>
+<DIV>
+This document describes the MX architecture, and how it has been
+ used in the Cinema-MX application. Its meant both as an overview of
+ the architecture, and also a introduction for those who might wish
+ to develop new modules for the application.
+</DIV>
+<P>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html10"
+ HREF="node1.html">Introduction</A>
+<LI><A NAME="tex2html11"
+ HREF="node2.html">Requirements</A>
+<LI><A NAME="tex2html12"
+ HREF="node3.html">Identifiers</A>
+<UL>
+<LI><A NAME="tex2html13"
+ HREF="node4.html">Abstract Identifiers</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html14"
+ HREF="node5.html">The Module</A>
+<UL>
+<LI><A NAME="tex2html15"
+ HREF="node6.html">Other methods</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html16"
+ HREF="node7.html">XML Loading and Configuration</A>
+<UL>
+<LI><A NAME="tex2html17"
+ HREF="node8.html">Loading</A>
+<LI><A NAME="tex2html18"
+ HREF="node9.html">Configuration</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html19"
+ HREF="node10.html">Cinema-MX Modules</A>
+<UL>
+<LI><A NAME="tex2html20"
+ HREF="node11.html">Cinema-MX modules in use</A>
+</UL>
+<BR>
+<LI><A NAME="tex2html21"
+ HREF="node12.html">Step by Step</A>
+<LI><A NAME="tex2html22"
+ HREF="node13.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/internals.pl b/doc/cinema-module/cinema-module/internals.pl
new file mode 100644
index 0000000..63a6941
--- /dev/null
+++ b/doc/cinema-module/cinema-module/internals.pl
@@ -0,0 +1,46 @@
+# LaTeX2HTML 2K.1beta (1.47)
+# Associate internals original text with physical files.
+
+
+$key = q/sec:module-1/;
+$ref_files{$key} = "$dir".q|node5.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:loading/;
+$ref_files{$key} = "$dir".q|node8.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:step-step/;
+$ref_files{$key} = "$dir".q|node12.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:cinema-modules-use/;
+$ref_files{$key} = "$dir".q|node11.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:cinema-modules/;
+$ref_files{$key} = "$dir".q|node10.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:configuration/;
+$ref_files{$key} = "$dir".q|node9.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:xml-load-conf/;
+$ref_files{$key} = "$dir".q|node7.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/tab:modules/;
+$ref_files{$key} = "$dir".q|node11.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:abstract-identifiers/;
+$ref_files{$key} = "$dir".q|node4.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:other-methods/;
+$ref_files{$key} = "$dir".q|node6.html|;
+$noresave{$key} = "$nosave";
+
+1;
+
diff --git a/doc/cinema-module/cinema-module/labels.pl b/doc/cinema-module/cinema-module/labels.pl
new file mode 100644
index 0000000..b65c2ff
--- /dev/null
+++ b/doc/cinema-module/cinema-module/labels.pl
@@ -0,0 +1,137 @@
+# LaTeX2HTML 2K.1beta (1.47)
+# Associate labels original text with physical files.
+
+
+$key = q/sec:module-1/;
+$external_labels{$key} = "$URL/" . q|node5.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:loading/;
+$external_labels{$key} = "$URL/" . q|node8.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:step-step/;
+$external_labels{$key} = "$URL/" . q|node12.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:cinema-modules-use/;
+$external_labels{$key} = "$URL/" . q|node11.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:cinema-modules/;
+$external_labels{$key} = "$URL/" . q|node10.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:configuration/;
+$external_labels{$key} = "$URL/" . q|node9.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:xml-load-conf/;
+$external_labels{$key} = "$URL/" . q|node7.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/tab:modules/;
+$external_labels{$key} = "$URL/" . q|node11.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:abstract-identifiers/;
+$external_labels{$key} = "$URL/" . q|node4.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:other-methods/;
+$external_labels{$key} = "$URL/" . q|node6.html|;
+$noresave{$key} = "$nosave";
+
+1;
+
+
+# LaTeX2HTML 2K.1beta (1.47)
+# labels from external_latex_labels array.
+
+
+$key = q/sec:module-1/;
+$external_latex_labels{$key} = q|4|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:trees/;
+$external_latex_labels{$key} = q|9|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:props/;
+$external_latex_labels{$key} = q|8|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:mod-load/;
+$external_latex_labels{$key} = q|7|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:ident/;
+$external_latex_labels{$key} = q|1|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:cinema-modules/;
+$external_latex_labels{$key} = q|6|;
+$noresave{$key} = "$nosave";
+
+$key = q/tab:modules/;
+$external_latex_labels{$key} = q|6.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:reqmod/;
+$external_latex_labels{$key} = q|5|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:other-methods/;
+$external_latex_labels{$key} = q|4.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:enum/;
+$external_latex_labels{$key} = q|2|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:reqident/;
+$external_latex_labels{$key} = q|4|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:step-step/;
+$external_latex_labels{$key} = q|7|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:loading/;
+$external_latex_labels{$key} = q|5.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:cinema-modules-use/;
+$external_latex_labels{$key} = q|6.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:cin-mod/;
+$external_latex_labels{$key} = q|11|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:xml-load-conf/;
+$external_latex_labels{$key} = q|5|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:ident-dir/;
+$external_latex_labels{$key} = q|6|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:configuration/;
+$external_latex_labels{$key} = q|5.2|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:config/;
+$external_latex_labels{$key} = q|10|;
+$noresave{$key} = "$nosave";
+
+$key = q/sec:abstract-identifiers/;
+$external_latex_labels{$key} = q|3.1|;
+$noresave{$key} = "$nosave";
+
+$key = q/lst:module/;
+$external_latex_labels{$key} = q|3|;
+$noresave{$key} = "$nosave";
+
+1;
+
diff --git a/doc/cinema-module/cinema-module/node1.html b/doc/cinema-module/cinema-module/node1.html
new file mode 100644
index 0000000..b2f2ae2
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node1.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Introduction</TITLE>
+<META NAME="description" CONTENT="Introduction">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node2.html">
+<LINK REL="previous" HREF="cinema-module.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node2.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html31"
+ HREF="node2.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html29"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html23"
+ HREF="cinema-module.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html32"
+ HREF="node2.html">Requirements</A>
+<B> Up:</B> <A NAME="tex2html30"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html24"
+ HREF="cinema-module.html">The MX architecture and</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00010000000000000000">
+Introduction</A>
+</H1>
+
+<P>
+The MX architecture was designed to allow Cinema-MX (or other
+applications) to be extended straightforwardly and simply. This is
+achieved by splitting the application up into a series of small
+modules. These modules can then be put together to form the end
+application.
+
+<P>
+For the Cinema-MX application as well as allowing modularity we wanted
+to gain extensibility, allowing the user to integrate new modules into
+Cinema-MX, without requiring alteration of the main code base. To this
+end, XML has been used to define which modules should be loaded, and
+also to provide some configuration for these modules if required.
+
+<P>
+In the following documentation I describe how the MX architecture
+works and what all the various bits do. If you can't be bothered to
+read this, then there is a very quick ``step-by-step'' guide in
+Section <A HREF="node12.html#sec:step-step">7</A>, which you might prefer.
+
+<P>
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node10.html b/doc/cinema-module/cinema-module/node10.html
new file mode 100644
index 0000000..3429476
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node10.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Cinema-MX Modules</TITLE>
+<META NAME="description" CONTENT="Cinema-MX Modules">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node12.html">
+<LINK REL="previous" HREF="node7.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node11.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html119"
+ HREF="node11.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html117"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html111"
+ HREF="node9.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html120"
+ HREF="node11.html">Cinema-MX modules in use</A>
+<B> Up:</B> <A NAME="tex2html118"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html112"
+ HREF="node9.html">Configuration</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00060000000000000000"></A>
+<A NAME="sec:cinema-modules"></A>
+<BR>
+Cinema-MX Modules
+</H1>
+
+<P>
+Although the MX architecture provides the ability to define modules,
+and their interaction with each other, they do not provide any
+specific Cinema functionality. It would be possible to provide all of
+this functionality through the MX system, by accessing specific
+modules. However for convenience the <TT><FONT SIZE="-1">XMLModule</FONT></TT> class has been
+extended, to give access to a number of different method, through the
+<TT><FONT SIZE="-1">CinemaModule</FONT></TT> class.
+<A NAME="tex2html1"
+ HREF="footnode.html#foot197"><SUP>1</SUP></A>Additionally there is a more specific <TT><FONT SIZE="-1">CinemaCoreGui</FONT></TT> class,
+which gives access to more methods, which gives direct access to the
+widgets used to build the basic Cinema-MX frame. Essentially the rule is
+extend the <TT><FONT SIZE="-1">CinemaModule</FONT></TT> unless you really need the
+<TT><FONT SIZE="-1">CinemaGuiModule</FONT></TT> as the latter is less likely to remain stable.
+
+<P>
+<PRE>[caption=The Cinema Module, label=lst:cin-mod]
+public abstract class CinemaModule extends XMLModule
+ implements AlignmentEventProvider
+
+ public SequenceAlignment getSequenceAlignment()
+ public void setSequenceAlignment( SequenceAlignment seq )
+ public ColorMap getColorMap()
+ public void setColorMap( ColorMap map )
+ public AlignmentSelectionModel getAlignmentSelectionModel()
+ public void setAlignmentSelectionModel( AlignmentSelectionModel model )
+ public void setSequenceTitleColor( GappedSequence seq, Color colour )
+ public void clearSequenceTitleColor( GappedSequence seq )
+ public void sendStatusMessage( String message )
+ // CinemaModule
+</PRE>
+
+<P>
+The interface of the <TT><FONT SIZE="-1">CinemaModule</FONT></TT> is shown in
+Listing <A HREF="#lst:cin-mod">11</A>. Direct access is provided to the alignment
+being shown, to the <TT><FONT SIZE="-1">ColorMap</FONT></TT>.
+<A NAME="tex2html2"
+ HREF="footnode.html#foot154"><SUP>2</SUP></A>The other methods give access to other information associated with the
+view, including the Selection Model, the colour associated with the
+sequence, and a status message which appears at the bottom of the
+Cinema-MX frame.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html121"
+ HREF="node11.html">Cinema-MX modules in use</A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html119"
+ HREF="node11.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html117"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html111"
+ HREF="node9.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html120"
+ HREF="node11.html">Cinema-MX modules in use</A>
+<B> Up:</B> <A NAME="tex2html118"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html112"
+ HREF="node9.html">Configuration</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node11.html b/doc/cinema-module/cinema-module/node11.html
new file mode 100644
index 0000000..cd51837
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node11.html
@@ -0,0 +1,225 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Cinema-MX modules in use</TITLE>
+<META NAME="description" CONTENT="Cinema-MX modules in use">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="previous" HREF="node10.html">
+<LINK REL="up" HREF="node10.html">
+<LINK REL="next" HREF="node12.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html128"
+ HREF="node12.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html126"
+ HREF="node10.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html122"
+ HREF="node10.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html129"
+ HREF="node12.html">Step by Step</A>
+<B> Up:</B> <A NAME="tex2html127"
+ HREF="node10.html">Cinema-MX Modules</A>
+<B> Previous:</B> <A NAME="tex2html123"
+ HREF="node10.html">Cinema-MX Modules</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00061000000000000000"></A>
+<A NAME="sec:cinema-modules-use"></A>
+<BR>
+Cinema-MX modules in use
+</H2>
+
+<P>
+The MX architecture works best if the individual <TT><FONT SIZE="-1">Module</FONT></TT>'s are
+relatively small. To give some idea of how this works in Cinema-MX, the
+<TT><FONT SIZE="-1">Module</FONT></TT>'s are described in Table <A HREF="node11.html#tab:modules">6.1</A>. Some of
+these are very small (100 lines or so), and some quite a bit larger,
+and use several other specialised classes.
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER"><A NAME="199"></A>
+<TABLE>
+<CAPTION><STRONG>Table:</STRONG>
+The modules in use within the Cinema-MX application. The
+ modules are organized by their super class, either the
+ <TT><FONT SIZE="-1">CinemaModule</FONT></TT>, the <TT><FONT SIZE="-1">CinemaGuiModule</FONT></TT>, or
+ <TT><FONT SIZE="-1">Others</FONT></TT>, which are extended from some other module. </CAPTION>
+<TR><TD> <TABLE CELLPADDING=3 BORDER="1">
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaModule</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Function</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaColorFactory</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Generates <TT><FONT SIZE="-1">ColorMap</FONT></TT> instances, and menu
+items for their selection.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaCommandLineParser</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Parses the command line, and acts on it.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaConsensus</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Provides calculation of consensus sequences</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaGroupModule</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Group sequences, for editing, viewing, and
+analysis.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaMenuBuilder</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Generate menu items on the basis of the XML
+configurations</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaMotifModule</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>The MotifManager dialog, and output</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaMultipleConsensusViewer</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>View consensus sequences of groups,
+and there variance.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaPersist</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Save information between instantiations of Cinema-MX</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaRegexp</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Regular Expression searches down sequences</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaResizeElements</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Resize sequence cells</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaSlaveViewerModule</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Generate viewer frames for use by other
+modules.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaSplash</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Adds massive functionality in the form of a Splash
+screen.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>FormGroupsByPrints</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350><B>Experimental!</B> Queries the PRINTS_S
+database to display the PRINTS motifs.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>PhylipInvoker</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350><B>Experimental!</B> Displays a phylogenetic
+tree.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaGuiModule</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350> </TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>AbstractSequenceInput</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Input sequence by some route.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>AbstractSequenceOutput</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Output sequence by some route.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaColorSelector</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Select <TT><FONT SIZE="-1">ColorMap</FONT></TT>.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaConsensusDisplay</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Displays the consensus sequences.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaCoreView</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Support for CinemaModule class</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaGo</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Well everybody hacks some times</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaHackMenu</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>More professionally displayed as ``in development''
+in the menu system. Its quicker to add here than through XML.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CineamMenuSystem</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Uses CinemaMenuBuilder to build menu, then displays
+it</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaSequenceMenu</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Right click on sequence button menu.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaStatusInformation</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Prints ``cursor here'' information in status
+bar.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>Others</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350> </TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaCoreGui</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Extends directly from the <TT><FONT SIZE="-1">Module</FONT></TT> class, and
+provides support for the CinemaGuiModule class.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>XMLBootModule</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Extends from directly from <TT><FONT SIZE="-1">Module</FONT></TT>. Loads1
+parsers for reading XML configuration.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaBoot</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Extends from <TT><FONT SIZE="-1">XMLBootModule</FONT></TT>. Additional support for
+Cinema-MX XML loading.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>CinemaFilePersist</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Extends from <TT><FONT SIZE="-1">CinemaPersist</FONT></TT>. Save
+persistence data to file.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>FileSequenceInput</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Extends from <TT><FONT SIZE="-1">AbstractSequenceInput</FONT></TT>.
+Load from file.</TD>
+</TR>
+<TR><TD ALIGN="LEFT" VALIGN="TOP" WIDTH=150>FileSequenceOutput</TD>
+<TD ALIGN="LEFT" VALIGN="TOP" WIDTH=350>Extends from <TT><FONT SIZE="-1">AbstractSequenceOutput</FONT></TT>.
+Save to file.</TD>
+</TR>
+</TABLE>
+ <A NAME="tab:modules"></A> </TD></TR>
+</TABLE>
+</DIV><P></P>
+<BR>
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html128"
+ HREF="node12.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html126"
+ HREF="node10.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html122"
+ HREF="node10.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html129"
+ HREF="node12.html">Step by Step</A>
+<B> Up:</B> <A NAME="tex2html127"
+ HREF="node10.html">Cinema-MX Modules</A>
+<B> Previous:</B> <A NAME="tex2html123"
+ HREF="node10.html">Cinema-MX Modules</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node12.html b/doc/cinema-module/cinema-module/node12.html
new file mode 100644
index 0000000..3d6060d
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node12.html
@@ -0,0 +1,122 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Step by Step</TITLE>
+<META NAME="description" CONTENT="Step by Step">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node13.html">
+<LINK REL="previous" HREF="node10.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node13.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html138"
+ HREF="node13.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html136"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html130"
+ HREF="node11.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html139"
+ HREF="node13.html">About this document ...</A>
+<B> Up:</B> <A NAME="tex2html137"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html131"
+ HREF="node11.html">Cinema-MX modules in use</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00070000000000000000"></A>
+<A NAME="sec:step-step"></A>
+<BR>
+Step by Step
+</H1>
+
+<P>
+
+<OL>
+<LI>Define a new identifier class. See for instance
+ <TT><FONT SIZE="-1"><TT><A NAME="tex2html4"
+ HREF="uk.ac.man.bioinf.apps.cinema.util.CinemaUtilityIdentifier">uk.ac.man.bioinf.apps.cinema.util.CinemaUtilityIdentifier</A></TT></FONT></TT>.
+ Make sure that you get the class name of your module correct. I tend
+ to group my identifiers into logical blocks, as loading identifiers
+ for modules that you don't actually use, has a very low overhead.
+</LI>
+<LI>Define a new module class. This can be very small. Take for
+ instance <TT><FONT SIZE="-1"> <TT><A NAME="tex2html5"
+ HREF="uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule">uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule</A></TT></FONT></TT> . This
+ module is used only by other modules. The
+ <TT><FONT SIZE="-1"><TT><A NAME="tex2html6"
+ HREF="uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation">uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation</A></TT></FONT></TT> is
+ a ``user-facing'' module, that is also very simple. It provides the
+ ``cursor information'' in the status bar.
+</LI>
+<LI>Write, or add to a ``main.xml''. This file should be placed in
+ ``./cinema/config''. This directory should already exist if you have
+ run Cinema-MX. This is a simple XML file with a top level tag of
+ ``configuration''. The DTD can be found in the Cinema-MX source.
+</LI>
+<LI>Load your identifier code. Listing <A HREF="#lst:ident-dir">6</A> shows how
+ to do this.
+</LI>
+<LI>Actually load and start the module. Listing <A HREF="#lst:mod-load">7</A>
+ shows how to do this.
+</LI>
+</OL>
+
+<P>
+And pretty much that should be it.
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html138"
+ HREF="node13.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html136"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html130"
+ HREF="node11.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html139"
+ HREF="node13.html">About this document ...</A>
+<B> Up:</B> <A NAME="tex2html137"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html131"
+ HREF="node11.html">Cinema-MX modules in use</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node13.html b/doc/cinema-module/cinema-module/node13.html
new file mode 100644
index 0000000..f40559f
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node13.html
@@ -0,0 +1,74 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>About this document ...</TITLE>
+<META NAME="description" CONTENT="About this document ...">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="previous" HREF="node12.html">
+<LINK REL="up" HREF="cinema-module.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next_g.png">
+<A NAME="tex2html144"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html140"
+ HREF="node12.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Up:</B> <A NAME="tex2html145"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html141"
+ HREF="node12.html">Step by Step</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00080000000000000000">
+About this document ...</A>
+</H1>
+ <STRONG>The MX architecture and its usage within
+ the Cinema-MX application</STRONG><P>
+This document was generated using the
+<A HREF="http://www-dsed.llnl.gov/files/programs/unix/latex2html/manual/"><STRONG>LaTeX</STRONG>2<tt>HTML</tt></A> translator Version 2K.1beta (1.47)
+<P>
+Copyright © 1993, 1994, 1995, 1996,
+<A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>,
+Computer Based Learning Unit, University of Leeds.
+<BR>
+Copyright © 1997, 1998, 1999,
+<A HREF="http://www.maths.mq.edu.au/~ross/">Ross Moore</A>,
+Mathematics Department, Macquarie University, Sydney.
+<P>
+The command line arguments were: <BR>
+ <STRONG>latex2html</STRONG> <TT><A NAME="tex2html7"
+ HREF="../cinema-module.tex">cinema-module.tex</A></TT>
+<P>
+The translation was initiated by Dr. Phillip Lord on 2002-04-20
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node2.html b/doc/cinema-module/cinema-module/node2.html
new file mode 100644
index 0000000..255155a
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node2.html
@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Requirements</TITLE>
+<META NAME="description" CONTENT="Requirements">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node3.html">
+<LINK REL="previous" HREF="node1.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node3.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html41"
+ HREF="node3.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html39"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html33"
+ HREF="node1.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html42"
+ HREF="node3.html">Identifiers</A>
+<B> Up:</B> <A NAME="tex2html40"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html34"
+ HREF="node1.html">Introduction</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00020000000000000000">
+Requirements</A>
+</H1>
+
+<P>
+There were a number of requirements for the MX architecture.
+
+<UL>
+<LI>The architecture should be relatively <I>light-weight</I>. That
+ is it should be verbose, which would discourage programmers from
+ making small modules.
+</LI>
+<LI>The basic architecture should be as customisable as possible.
+</LI>
+<LI>The architecture should be <I>fail fast</I>, that is it should
+ break early, rather than run incorrectly.
+</LI>
+<LI>Dependency between modules should be explicit.
+</LI>
+<LI>Loading should be as rapid as possible.
+</LI>
+</UL>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node3.html b/doc/cinema-module/cinema-module/node3.html
new file mode 100644
index 0000000..955b8df
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node3.html
@@ -0,0 +1,157 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Identifiers</TITLE>
+<META NAME="description" CONTENT="Identifiers">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node5.html">
+<LINK REL="previous" HREF="node2.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node4.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html51"
+ HREF="node4.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html49"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html43"
+ HREF="node2.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html52"
+ HREF="node4.html">Abstract Identifiers</A>
+<B> Up:</B> <A NAME="tex2html50"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html44"
+ HREF="node2.html">Requirements</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00030000000000000000">
+Identifiers</A>
+</H1>
+
+<P>
+The requirement that module dependency should be explicit creates a
+problem. One module must be able to refer to another. However if that
+class is referred to directly, then the class will be loaded
+immediately, when we might want to defer it.
+
+<P>
+To circumvent this problem, we use an identifier class, which can be
+used to refer to the module, the interface for this is shown in
+Listing <A HREF="#lst:ident">1</A>.
+
+<P>
+<PRE>[label=lst:ident, caption=The ModuleIdentifier Interface]
+public interface ModuleIdentifier
+
+ public boolean isInterface();
+ public String getClassName();
+ public String getModuleName();
+// ModuleIdentifier
+</PRE>
+
+<P>
+The two methods in this interface <TT><FONT SIZE="-1">public String getClassName()</FONT></TT>
+and <TT><FONT SIZE="-1">public String getModuleName()</FONT></TT> define the link between a
+module and a String which can be used to refer to it, which solves the
+problem of referring to a Module (by a name) and a Class.
+
+<P>
+One difficulty with this is that using a String (the module name) to
+refer to a module is not type safe, and will result in errors when the
+name is typed incorrectly. This difficulty is solved by extending the
+class <TT><FONT SIZE="-1">AbstractEnumeratedModuleIdentifier</FONT></TT>. This uses the a
+variation of the theme of the Singleton design pattern to create an
+identifier class which is relatively type safe. An example of its
+usage from Cinema-MX is shown in Listing <A HREF="#lst:enum">2</A>. This class uses
+reflection to translate the variable name of its instances, into the
+String that it uses for its Module name.
+
+<P>
+<PRE>[label=lst:enum, caption=The Abstract EnumeratedModuleIdentifier]
+public class CinemaBootIdentifier extends AbstractEnumeratedModuleIdentifier
+
+ private CinemaBootIdentifier( String className, String toString )
+
+ super( className, toString );
+
+ public static final CinemaBootIdentifier CINEMA_BOOT =
+ new CinemaBootIdentifier( "uk.ac.man.bioinf.apps.cinema.CinemaBoot",
+ "Main Cinema Boot Class" );
+ public static final CinemaBootIdentifier CINEMA_SHARED =
+ new CinemaBootIdentifier( "uk.ac.man.bioinf.apps.cinema.CinemaShared",
+ "Shared Boot Class" );
+ // CinemaBootIdentifier
+</PRE>
+
+<P>
+The practical upshot of all of this is that to refer to for instance
+the main Cinema Boot Module, the CINEMA_BOOT instance can be used
+directly. Its still possible to type this incorrectly of course, but
+this will be detected at compile time. Its also possible to type the
+class name incorrectly when writing the identifier, but at least this
+needs to only be done once.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html53"
+ HREF="node4.html">Abstract Identifiers</A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html51"
+ HREF="node4.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html49"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html43"
+ HREF="node2.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html52"
+ HREF="node4.html">Abstract Identifiers</A>
+<B> Up:</B> <A NAME="tex2html50"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html44"
+ HREF="node2.html">Requirements</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node4.html b/doc/cinema-module/cinema-module/node4.html
new file mode 100644
index 0000000..ebf59ad
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node4.html
@@ -0,0 +1,75 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Abstract Identifiers</TITLE>
+<META NAME="description" CONTENT="Abstract Identifiers">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="previous" HREF="node3.html">
+<LINK REL="up" HREF="node3.html">
+<LINK REL="next" HREF="node5.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html60"
+ HREF="node5.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html58"
+ HREF="node3.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html54"
+ HREF="node3.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html61"
+ HREF="node5.html">The Module</A>
+<B> Up:</B> <A NAME="tex2html59"
+ HREF="node3.html">Identifiers</A>
+<B> Previous:</B> <A NAME="tex2html55"
+ HREF="node3.html">Identifiers</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00031000000000000000"></A>
+<A NAME="sec:abstract-identifiers"></A>
+<BR>
+Abstract Identifiers
+</H2>
+
+<P>
+There is a final method in the <TT><FONT SIZE="-1">ModuleIdentifier</FONT></TT> class, called
+<TT><FONT SIZE="-1">isInteface</FONT></TT>. Normally this will return false, but it is possible
+to define a module which acts like an abstract class, and delegates
+its functionality to another module. This allows a degree of
+polymorphism for modules. This feature is not used very widely within
+Cinema-MX, as it turned out to be less needed than it appeared to be
+during design. For most purposes its easier to use ``Optional
+Modules'' which are described in Section <A HREF="node5.html#sec:module-1">4</A>.
+
+<P>
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node5.html b/doc/cinema-module/cinema-module/node5.html
new file mode 100644
index 0000000..3acc751
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node5.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>The Module</TITLE>
+<META NAME="description" CONTENT="The Module">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node7.html">
+<LINK REL="previous" HREF="node3.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node6.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html70"
+ HREF="node6.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html68"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html62"
+ HREF="node4.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html71"
+ HREF="node6.html">Other methods</A>
+<B> Up:</B> <A NAME="tex2html69"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html63"
+ HREF="node4.html">Abstract Identifiers</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00040000000000000000"></A>
+<A NAME="sec:module-1"></A>
+<BR>
+The Module
+</H1>
+
+<P>
+The <TT><FONT SIZE="-1">ModuleIdentifier</FONT></TT>interface refers to a Class name. This
+Class should be a instance of the <TT><FONT SIZE="-1">Module</FONT></TT> class. Its interface
+is shown in Listing <A HREF="#lst:module">3</A>. There are quite a few other
+methods in this class, but most of them have been elided here for the
+sake of simplicity.
+
+<P>
+<PRE>[label=lst:module,caption=The Module class]
+public abstract class Module
+
+ public void load() throws ModuleException ;
+ public void start();
+ public void destroy();
+ public ModuleIdentifierList getRequiredIdentifiers();
+ public Module getRequiredModule( ModuleIdentifier ident );
+ public abstract String getVersion();
+ // Module
+</PRE>
+
+<P>
+We can divide the methods shown here into three groups.
+
+<UL>
+<LI>Those related to dependency with other modules.
+</LI>
+<LI>Those directly to do with the function of the Module.
+</LI>
+<LI>And the other method.
+</LI>
+</UL>
+
+<P>
+Dealing with this in order. One of the requirements is for explicit
+dependency between modules. This is provided by the
+<TT><FONT SIZE="-1">public ModuleIdentifierList getRequiredIdentifiers()</FONT></TT> method. In
+this method any modules which this module depends on should be
+identified. For example, see Listing <A HREF="#lst:reqident">4</A>, which comes
+from the <TT><FONT SIZE="-1">CinemaConsensusDisplay</FONT></TT> module. This requires two other
+modules, namely <TT><FONT SIZE="-1">CinemaConsensus</FONT></TT>, which actually takes on the
+task of calculating the consensus, and <TT><FONT SIZE="-1">CinemaSystemEvents</FONT></TT>. The
+consensus display is threaded, and needs to know when the application
+is about to close, so that it can shut down cleanly.
+
+<P>
+<PRE>[label=lst:reqident, caption=An example of getRequiredIdentifiers]
+public ModuleIdentifierList getRequiredIdentifiers()
+
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaConsensusIdentifier.CINEMA_CONSENSUS );
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+
+</PRE>
+
+<P>
+The second method <TT><FONT SIZE="-1">public Module
+getRequiredModule(ModuleIdentifier ident)</FONT></TT> actually allows access to
+these modules. Listing <A HREF="#lst:reqmod">5</A> comes again from the
+<TT><FONT SIZE="-1">CinemaConsensusDisplay</FONT></TT> class
+
+<P>
+<PRE>[label=lst:reqmod, caption=An example of getRequiredModule]
+if( queue == null )
+ queue = new InvokerInternalQueue
+ ( (CinemaSystemEvents)getRequiredModule
+ ( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS ) );
+
+</PRE>
+
+<P>
+The methods dealing with module functionality are hopefully largely
+self-explanatory. When the module is initially loaded, unsurprising
+the <TT><FONT SIZE="-1">public void load</FONT></TT> method is called. During this time the
+module should perform any initialisation that is required. The rule at
+this time is that only initialisation that does not require other
+modules should be performed, as this may well not be available yet. Or
+in another way, while the <TT><FONT SIZE="-1">load()</FONT></TT> method is running, there are
+no guarantee's about what the <TT><FONT SIZE="-1">getRequiredModule()</FONT></TT> method will
+return (most likely it will return <TT><FONT SIZE="-1">null</FONT></TT>).
+
+<P>
+Immediately after this time the <TT><FONT SIZE="-1">public void start()</FONT></TT> method will
+be called. At this time it is guaranteed that the
+<TT><FONT SIZE="-1">getRequiredModule()</FONT></TT> method will return any of the Modules
+identified, and that further all of their <TT><FONT SIZE="-1">load()</FONT></TT> methods will
+have been called and have successfully completed.
+
+<P>
+This is actually simpler than it sounds, but it's designed to cope
+with a fairly complex dependency graph, and generally it just
+works. No checking is performed to ensure that the graph is acyclic
+The system will crash if you do this, but as per the design
+requirement it will fail immediately.
+
+<P>
+And finally the other method. This is meant to return a String
+identifying the version of the Module. This is not widely used. No
+specific semantics is required for this String, and generally the CVS
+version keyword has been used. This might be removed at a later date.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html72"
+ HREF="node6.html">Other methods</A>
+</UL>
+<!--End of Table of Child-Links-->
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html70"
+ HREF="node6.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html68"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html62"
+ HREF="node4.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html71"
+ HREF="node6.html">Other methods</A>
+<B> Up:</B> <A NAME="tex2html69"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html63"
+ HREF="node4.html">Abstract Identifiers</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node6.html b/doc/cinema-module/cinema-module/node6.html
new file mode 100644
index 0000000..b36201e
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node6.html
@@ -0,0 +1,81 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Other methods</TITLE>
+<META NAME="description" CONTENT="Other methods">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="previous" HREF="node5.html">
+<LINK REL="up" HREF="node5.html">
+<LINK REL="next" HREF="node7.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html79"
+ HREF="node7.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html77"
+ HREF="node5.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html73"
+ HREF="node5.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html80"
+ HREF="node7.html">XML Loading and Configuration</A>
+<B> Up:</B> <A NAME="tex2html78"
+ HREF="node5.html">The Module</A>
+<B> Previous:</B> <A NAME="tex2html74"
+ HREF="node5.html">The Module</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00041000000000000000"></A>
+<A NAME="sec:other-methods"></A>
+<BR>
+Other methods
+</H2>
+
+<P>
+There are a few other methods which are potentially of interest within
+the <TT><FONT SIZE="-1">Module</FONT></TT> interface. Firstly the <TT><FONT SIZE="-1">Module</FONT></TT> provides access
+to the <TT><FONT SIZE="-1">ModuleContext</FONT></TT> class, which contains the <TT><FONT SIZE="-1">public
+Module getModule(ModuleIdentifier ident)</FONT></TT>. This enables access to
+any other Modules in the system, beyond those named as required
+modules. As they are not required they may be unavailable, so checking
+the <TT><FONT SIZE="-1">public boolean isModuleAvailable(ModuleIdentifier
+identifier)</FONT></TT> first is probably wise.
+
+<P>
+And finally the <TT><FONT SIZE="-1">ModuleContext</FONT></TT> class gives access to the
+<TT><FONT SIZE="-1">public Object getConfig()</FONT></TT> method. Of itself this is not that
+useful. Its used internally to provide XML configuration though, which
+is described in Section <A HREF="node9.html#sec:configuration">5.2</A>.
+
+<P>
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node7.html b/doc/cinema-module/cinema-module/node7.html
new file mode 100644
index 0000000..8a61a02
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node7.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>XML Loading and Configuration</TITLE>
+<META NAME="description" CONTENT="XML Loading and Configuration">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node10.html">
+<LINK REL="previous" HREF="node5.html">
+<LINK REL="up" HREF="cinema-module.html">
+<LINK REL="next" HREF="node8.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html89"
+ HREF="node8.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html87"
+ HREF="cinema-module.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html81"
+ HREF="node6.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html90"
+ HREF="node8.html">Loading</A>
+<B> Up:</B> <A NAME="tex2html88"
+ HREF="cinema-module.html">The MX architecture and</A>
+<B> Previous:</B> <A NAME="tex2html82"
+ HREF="node6.html">Other methods</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00050000000000000000"></A>
+<A NAME="sec:xml-load-conf"></A>
+<BR>
+XML Loading and Configuration
+</H1>
+
+<P>
+The module system described so far provides a basic
+architecture. However some mechanism needs to be available to define
+which modules should be used. While it is possible to do this using
+Java directly this would require the user to possess a Java compiler
+to enable new modules, or reconfigure existing ones. By defining the
+loading and configuration in XML, it's possible to do this using a
+text editor.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html91"
+ HREF="node8.html">Loading</A>
+<LI><A NAME="tex2html92"
+ HREF="node9.html">Configuration</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node8.html b/doc/cinema-module/cinema-module/node8.html
new file mode 100644
index 0000000..f8b8c8d
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node8.html
@@ -0,0 +1,130 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Loading</TITLE>
+<META NAME="description" CONTENT="Loading">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="next" HREF="node9.html">
+<LINK REL="previous" HREF="node7.html">
+<LINK REL="up" HREF="node7.html">
+<LINK REL="next" HREF="node9.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html101"
+ HREF="node9.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html99"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html93"
+ HREF="node7.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html102"
+ HREF="node9.html">Configuration</A>
+<B> Up:</B> <A NAME="tex2html100"
+ HREF="node7.html">XML Loading and Configuration</A>
+<B> Previous:</B> <A NAME="tex2html94"
+ HREF="node7.html">XML Loading and Configuration</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00051000000000000000"></A>
+<A NAME="sec:loading"></A>
+<BR>
+Loading
+</H2>
+
+<P>
+As described in Section <A HREF="node4.html#sec:abstract-identifiers">3.1</A>, each module
+referred to by a <TT><FONT SIZE="-1">ModuleIdentifier</FONT></TT>. In order to load first the
+ModuleIdentifier must be made available to the system.
+The <TT><FONT SIZE="-1">Identifier</FONT></TT> directive can be used to this end, as shown in
+Listing <A HREF="#lst:ident-dir">6</A>. This code assumes that the
+<TT><FONT SIZE="-1">AbstractEnumeratedModuleIdentifier</FONT></TT> has been used. For further
+information see the <TT><FONT SIZE="-1">module.dtd</FONT></TT> file in the source, which is
+heavily documented. Its worth remembering that the
+<TT><FONT SIZE="-1">AbstractEnumeratedModuleIdentifier</FONT></TT> can contain identifiers for
+many different modules, so relatively few of these statements are
+needed. In Cinema-MX the modules are grouped into functional units. The
+overhead of loading an <TT><FONT SIZE="-1">ModuleIdentifier</FONT></TT> is very low (a few objects
+for each additional one), so there is not really any problem in
+loading these, even if the module is not used in the end.
+
+<P>
+<PRE>[language=HTML, caption=The Identifier Directive, label=lst:ident-dir]
+<identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier</class>
+ </enumeration>
+</identifier>
+</PRE>
+
+<P>
+Having made the <TT><FONT SIZE="-1">ModuleIdentifier</FONT></TT> available, the module itself
+can be loaded or started from within the XML, using the <TT><FONT SIZE="-1">load</FONT></TT>
+and <TT><FONT SIZE="-1">start</FONT></TT> directive. The module is referred to by the name
+returned by the identifier. For example, the code
+in <A HREF="#lst:mod-load">7</A> shows loading and starting of the module that
+provides the ``status bar'' in Cinema-MX.
+
+<P>
+<PRE>[language=HTML, caption=Loading a Module, label=lst:mod-load]
+<load>
+ <name>CINEMA_STATUS</name>
+</load>
+<start>
+ <name>CINEMA_STATUS</name>
+</start>
+</PRE>
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html101"
+ HREF="node9.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html99"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html93"
+ HREF="node7.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html102"
+ HREF="node9.html">Configuration</A>
+<B> Up:</B> <A NAME="tex2html100"
+ HREF="node7.html">XML Loading and Configuration</A>
+<B> Previous:</B> <A NAME="tex2html94"
+ HREF="node7.html">XML Loading and Configuration</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/cinema-module/node9.html b/doc/cinema-module/cinema-module/node9.html
new file mode 100644
index 0000000..00d4f25
--- /dev/null
+++ b/doc/cinema-module/cinema-module/node9.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.47)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Configuration</TITLE>
+<META NAME="description" CONTENT="Configuration">
+<META NAME="keywords" CONTENT="cinema-module">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="cinema-module.css">
+
+<LINK REL="previous" HREF="node8.html">
+<LINK REL="up" HREF="node7.html">
+<LINK REL="next" HREF="node10.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html109"
+ HREF="node10.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html107"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html103"
+ HREF="node8.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html110"
+ HREF="node10.html">Cinema-MX Modules</A>
+<B> Up:</B> <A NAME="tex2html108"
+ HREF="node7.html">XML Loading and Configuration</A>
+<B> Previous:</B> <A NAME="tex2html104"
+ HREF="node8.html">Loading</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00052000000000000000"></A>
+<A NAME="sec:configuration"></A>
+<BR>
+Configuration
+</H2>
+
+<P>
+As well as loading modules its also possible to configure them. At the
+current time, the configuration can come in one of two forms, which
+are a properties list, or a tree structure. For example in
+Listing <A HREF="#lst:props">8</A> the configuration which is used for input
+module, is shown. It defines ``parsers'' which are used to output
+sequence data. This configurability means that it's to possible to add
+new ``parsers'' (perhaps inappropriately named as they are used for
+both input and output of sequences) Cinema-MX, by altering the
+configuration for this module.
+
+<P>
+<PRE>[label=lst:props, caption=Configuring Parsers]
+<properties>
+ <paramname>PIR</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser</value>
+ </param>
+ <param>
+ <paramname>MOT</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.MotProteinParser</value>
+ </param>
+</properties>
+</PRE>
+
+<P>
+The second type of configuration is a simple tree structure, which
+can be seen in Listing <A HREF="#lst:trees">9</A>. In this case the menu system
+is being configured. In this case most of the configuration has been
+elided. Generally speaking the properties configuration is to be
+preferred because its much simpler, but the tree structure is much
+more versatile, and means that tricks, such as providing additional
+semantics to the keys of the properties lists are not necessary.
+
+<P>
+<PRE>[language=HTML, caption=Configuring the menu system, label=lst:trees]
+<tree>
+ <!- The File Menu ->
+ <node>
+ <value>File</value>
+ <node>
+ <!- Provides the open alignment ->
+ <name>SEQ_INPUT</name>
+ </node>
+ <node>
+ <!- Provides the save alignment ->
+ <name>SEQ_OUTPUT</name>
+ </node>
+ <node>
+ <!- Provides the exit menu ->
+ <name>CINEMA_CORE_GUI</name>
+ </node>
+ </node>
+</tree>
+</PRE>
+
+<P>
+In order for the modules to access this configuration two methods (see
+Listing <A HREF="#lst:config">10</A>) are provided by the <TT><FONT SIZE="-1">XMLModule</FONT></TT> class
+which all the Cinema-MX modules extend from. The standard Java
+<TT><FONT SIZE="-1">Properties</FONT></TT> class has been used here. Sadly Java does not
+provide a standard Tree class, so a simple one has been provided.
+
+<P>
+<PRE>[label=lst:config, caption=The XML methods]
+public Properties getConfigProperties();
+public ConfigNode getConfigTree();
+</PRE>
+
+<P>
+<HR>
+<!--Navigation Panel-->
+<A NAME="tex2html109"
+ HREF="node10.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="file:/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html107"
+ HREF="node7.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="file:/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html103"
+ HREF="node8.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="file:/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html110"
+ HREF="node10.html">Cinema-MX Modules</A>
+<B> Up:</B> <A NAME="tex2html108"
+ HREF="node7.html">XML Loading and Configuration</A>
+<B> Previous:</B> <A NAME="tex2html104"
+ HREF="node8.html">Loading</A>
+<!--End of Navigation Panel-->
+<ADDRESS>
+Dr. Phillip Lord
+2002-04-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/doc/cinema-module/listings.perl b/doc/cinema-module/listings.perl
new file mode 100644
index 0000000..ab6848a
--- /dev/null
+++ b/doc/cinema-module/listings.perl
@@ -0,0 +1,12 @@
+package main;
+
+
+
+sub do_cmd_lstset{
+}
+
+sub do_env_lstlisting {
+ return "<PRE>" . @_[ 0 ] . "</PRE>";
+}
+
+1;
diff --git a/doc/cinema-module/missfont.log b/doc/cinema-module/missfont.log
new file mode 100644
index 0000000..075dc3b
--- /dev/null
+++ b/doc/cinema-module/missfont.log
@@ -0,0 +1,84 @@
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmri7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmri7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmri7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmri7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmb7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
+mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 ptmr7t
diff --git a/doc/javadoc/allclasses-frame.html b/doc/javadoc/allclasses-frame.html
new file mode 100644
index 0000000..c73c800
--- /dev/null
+++ b/doc/javadoc/allclasses-frame.html
@@ -0,0 +1,777 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:07 BST 2002 -->
+<TITLE>
+All Classes
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="All Classes";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameHeadingFont">
+<B>All Classes</B></FONT>
+<BR>
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html" TARGET="classFrame">AbstractComplexSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html" TARGET="classFrame">AbstractComplexSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html" TARGET="classFrame">AbstractDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html" TARGET="classFrame">AbstractEditableSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html" TARGET="classFrame">AbstractElement</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html" TARGET="classFrame">AbstractEnumeratedModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html" TARGET="classFrame">AbstractEnumeratedSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html" TARGET="classFrame">AbstractEnumeration</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html" TARGET="classFrame">AbstractEnumeration.ElementIterator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html" TARGET="classFrame">AbstractGappedSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html" TARGET="classFrame">AbstractGappedSequenceGroup</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html" TARGET="classFrame">AbstractIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html" TARGET="classFrame">AbstractMutableSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html" TARGET="classFrame">AbstractProteinAlignmentInputParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html" TARGET="classFrame">AbstractProteinSequenceInputParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html" TARGET="classFrame">AbstractSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html" TARGET="classFrame">AbstractSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html" TARGET="classFrame">AbstractSequenceInput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html" TARGET="classFrame">AbstractSequenceInputParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html" TARGET="classFrame">AbstractSequenceOutput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html" TARGET="classFrame">AbstractSequenceParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html" TARGET="classFrame">AbstractSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html" TARGET="classFrame">AlignmentColumn</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html" TARGET="classFrame">AlignmentEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html" TARGET="classFrame"><I>AlignmentEventProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html" TARGET="classFrame">AlignmentEventType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html" TARGET="classFrame"><I>AlignmentInputParser</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html" TARGET="classFrame"><I>AlignmentListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html" TARGET="classFrame">AlignmentListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html" TARGET="classFrame"><I>AlignmentOutputParser</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html" TARGET="classFrame">AlignmentParserInputTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html" TARGET="classFrame">AlignmentParserIOTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html" TARGET="classFrame">AlignmentRulerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html" TARGET="classFrame">AlignmentSelectionEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html" TARGET="classFrame"><I>AlignmentSelectionListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html" TARGET="classFrame">AlignmentSelectionListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html" TARGET="classFrame"><I>AlignmentSelectionModel</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html" TARGET="classFrame"><I>AlignmentSelectionRenderer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html" TARGET="classFrame">AlignmentToListCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html" TARGET="classFrame">AlignmentToListModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html" TARGET="classFrame">AlignmentVetoException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html" TARGET="classFrame"><I>AlignmentViewerCellRenderer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html" TARGET="classFrame">AlignmentViewerTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html" TARGET="classFrame">AlignmentViewerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html" TARGET="classFrame">AminoAcid</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html" TARGET="classFrame">AminoAcidColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html" TARGET="classFrame">AnonInvoker</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html" TARGET="classFrame">ApplicationFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html" TARGET="classFrame">ArrayManipulation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html" TARGET="classFrame">BasicAlignmentRulerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html" TARGET="classFrame">BasicAlignmentViewerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html" TARGET="classFrame">BasicWindowMonitor</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html" TARGET="classFrame">BorderFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html" TARGET="classFrame">ButtonPanelTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html" TARGET="classFrame">ButtonViewerPopupMenu</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html" TARGET="classFrame">CalculatePercentageID</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html" TARGET="classFrame">CellRendererPaneReplacement</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/Changeable.html" TARGET="classFrame"><I>Changeable</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html" TARGET="classFrame">ChangeableEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ChangeableListener.html" TARGET="classFrame"><I>ChangeableListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html" TARGET="classFrame">ChangeableListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html" TARGET="classFrame">ChangeListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html" TARGET="classFrame">CheckMotifLocationAgainstPrints</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html" TARGET="classFrame">ChunkyListModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html" TARGET="classFrame">Cinema</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html" TARGET="classFrame"><I>CinemaActionProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html" TARGET="classFrame">CinemaAlignmentFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html" TARGET="classFrame">CinemaAnchorManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html" TARGET="classFrame">CinemaBoot</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html" TARGET="classFrame">CinemaBootIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html" TARGET="classFrame">CinemaColorFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html" TARGET="classFrame">CinemaColorIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html" TARGET="classFrame">CinemaColorSelector</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html" TARGET="classFrame">CinemaCommandLineParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html" TARGET="classFrame">CinemaCommandLineParserIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html" TARGET="classFrame">CinemaConsensus</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html" TARGET="classFrame"><I>CinemaConsensusCalculatorMetaData</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html" TARGET="classFrame">CinemaConsensusDisplay</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html" TARGET="classFrame">CinemaConsensusIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html" TARGET="classFrame">CinemaCoreGui</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html" TARGET="classFrame">CinemaCoreIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html" TARGET="classFrame">CinemaCoreView</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html" TARGET="classFrame">CinemaDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html" TARGET="classFrame">CinemaDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html" TARGET="classFrame">CinemaFileOptionableExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html" TARGET="classFrame">CinemaFilePersist</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html" TARGET="classFrame"><I>CinemaFramedActionProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html" TARGET="classFrame">CinemaGo</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html" TARGET="classFrame">CinemaGroup</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html" TARGET="classFrame">CinemaGroupFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html" TARGET="classFrame">CinemaGroupIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html" TARGET="classFrame">CinemaGroupManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html" TARGET="classFrame">CinemaGroupModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html" TARGET="classFrame">CinemaGuiModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html" TARGET="classFrame">CinemaInvoker</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html" TARGET="classFrame">CinemaMenuBuilder</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html" TARGET="classFrame">CinemaMenuSystem</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html" TARGET="classFrame">CinemaModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html" TARGET="classFrame">CinemaModuleCoreIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html" TARGET="classFrame">CinemaModuleFactoryInstance</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html" TARGET="classFrame">CinemaMotifFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html" TARGET="classFrame">CinemaMotifIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html" TARGET="classFrame">CinemaMotifModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html" TARGET="classFrame">CinemaMultipleConsensusViewer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html" TARGET="classFrame">CinemaPersist</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html" TARGET="classFrame">CinemaProperties</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html" TARGET="classFrame">CinemaRegexp</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html" TARGET="classFrame">CinemaResizeElements</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html" TARGET="classFrame">CinemaResources</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html" TARGET="classFrame">CinemaSequenceMenu</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html" TARGET="classFrame">CinemaShared</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html" TARGET="classFrame">CinemaSharedIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html" TARGET="classFrame">CinemaSharedQuitExit</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html" TARGET="classFrame">CinemaSlaveViewerModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html" TARGET="classFrame">CinemaSplash</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html" TARGET="classFrame">CinemaStatusInformation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html" TARGET="classFrame">CinemaSystemEvents</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html" TARGET="classFrame">CinemaTestLaunch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html" TARGET="classFrame">CinemaTestModuleLaunch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html" TARGET="classFrame">CinemaUtilityIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html" TARGET="classFrame">CinemaXMLParserFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html" TARGET="classFrame">CollectionPrinter</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html" TARGET="classFrame">ColorFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html" TARGET="classFrame">ColorGenerator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html" TARGET="classFrame">ColorList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html" TARGET="classFrame"><I>ColorMap</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html" TARGET="classFrame">ColormapColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html" TARGET="classFrame">ColorMapException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html" TARGET="classFrame"><I>ColorMapMetaData</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorStore.html" TARGET="classFrame">ColorStore</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html" TARGET="classFrame"><I>ComplexEditableGappedSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html" TARGET="classFrame"><I>ComplexElement</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html" TARGET="classFrame">ComplexElementAndModificationTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html" TARGET="classFrame">ComplexElementFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html" TARGET="classFrame"><I>ComplexElementFactoryInterface</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html" TARGET="classFrame"><I>ComplexSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html" TARGET="classFrame">ComplexSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html" TARGET="classFrame"><I>ComplexSequenceType</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html" TARGET="classFrame">ConfigNode</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html" TARGET="classFrame"><I>ConsensusCalculator</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html" TARGET="classFrame">ConsensusIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html" TARGET="classFrame">ConsensusPercentageIDColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html" TARGET="classFrame"><I>ConsensusSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html" TARGET="classFrame">CursorLessFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html" TARGET="classFrame">DatabaseIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/Debug.html" TARGET="classFrame">Debug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html" TARGET="classFrame"><I>DebugInterface</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html" TARGET="classFrame">DebugMultiplexer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html" TARGET="classFrame">DecimalField</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html" TARGET="classFrame">DefaultAlignmentSelectionRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html" TARGET="classFrame">DefaultAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html" TARGET="classFrame">DefaultColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html" TARGET="classFrame">DefaultComplexElement</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html" TARGET="classFrame">DefaultComplexSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html" TARGET="classFrame">DefaultComplexSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html" TARGET="classFrame">DefaultConsensusSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html" TARGET="classFrame">DefaultDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html" TARGET="classFrame">DefaultEditableSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html" TARGET="classFrame">DefaultFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html" TARGET="classFrame">DefaultFileDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html" TARGET="classFrame">DefaultGappedComplexSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html" TARGET="classFrame">DefaultGappedSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html" TARGET="classFrame">DefaultGappedSequenceGroup</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html" TARGET="classFrame">DefaultModuleContext</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html" TARGET="classFrame">DefaultModuleFactoryInstance</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html" TARGET="classFrame">DefaultParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html" TARGET="classFrame">DefaultSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html" TARGET="classFrame">DefaultSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html" TARGET="classFrame">DefaultSequenceCursor</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html" TARGET="classFrame">DefaultXMLParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/Direction.html" TARGET="classFrame">Direction</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html" TARGET="classFrame">DNANucleotide</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/DNAResidue.html" TARGET="classFrame"><I>DNAResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html" TARGET="classFrame">DNASequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html" TARGET="classFrame">DoubleArrayColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html" TARGET="classFrame"><I>EditableSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html" TARGET="classFrame">EditableSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Element.html" TARGET="classFrame"><I>Element</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html" TARGET="classFrame">EmptyGappedSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html" TARGET="classFrame">EmptySequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html" TARGET="classFrame">EmptySequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html" TARGET="classFrame">EmptySequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html" TARGET="classFrame"><I>ExceptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html" TARGET="classFrame">ExpasySequenceRetriever</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html" TARGET="classFrame"><I>FastAlignmentViewerCellRenderer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html" TARGET="classFrame">FastaSequenceParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html" TARGET="classFrame">FetchSequenceBySwissProtID</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html" TARGET="classFrame">FileSaveableOptions</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html" TARGET="classFrame">FileSequenceInput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html" TARGET="classFrame">FileSequenceInputParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html" TARGET="classFrame">FileSequenceOutput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html" TARGET="classFrame">FileSequenceParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html" TARGET="classFrame">FileSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html" TARGET="classFrame">FormattedDocument</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html" TARGET="classFrame">Gap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html" TARGET="classFrame">GappableSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html" TARGET="classFrame"><I>GappedComplexSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html" TARGET="classFrame"><I>GappedSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html" TARGET="classFrame">GappedSequenceCharacterIterator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html" TARGET="classFrame"><I>GappedSequenceGroup</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html" TARGET="classFrame">GappedSequenceSearch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html" TARGET="classFrame">GappedSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html" TARGET="classFrame">GenericModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html" TARGET="classFrame">GrayScaleVariance</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html" TARGET="classFrame">GroupSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html" TARGET="classFrame">HardModificationSetFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html" TARGET="classFrame"><I>Identifiable</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html" TARGET="classFrame"><I>Identifier</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html" TARGET="classFrame">IllegalDuplicateModificationException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html" TARGET="classFrame">IndividualElementColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html" TARGET="classFrame">Install</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html" TARGET="classFrame">InstancePerAlignmentColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/IntArrayList.html" TARGET="classFrame">IntArrayList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html" TARGET="classFrame">IntegerField</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html" TARGET="classFrame">IntenseColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html" TARGET="classFrame">InvalidSequenceTypeException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html" TARGET="classFrame">InvalidSequenceTypeParserException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html" TARGET="classFrame">InvertedScrollPaneLayout</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html" TARGET="classFrame">Invoker</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html" TARGET="classFrame">InvokerInternalEventQueueException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html" TARGET="classFrame">InvokerInternalQueue</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html" TARGET="classFrame">InvokerInternalQueueException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html" TARGET="classFrame">InvokerThreadManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html" TARGET="classFrame">JAlignmentButtonPanel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html" TARGET="classFrame">JAlignmentRuler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html" TARGET="classFrame">JAlignmentViewer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html" TARGET="classFrame">JChangedScrollPane</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html" TARGET="classFrame">JLayableScrollPane</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html" TARGET="classFrame">Js_TestColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html" TARGET="classFrame">MalformedAccessionException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html" TARGET="classFrame">MetalAlignmentViewerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html" TARGET="classFrame">Methylation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html" TARGET="classFrame"><I>Modification</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html" TARGET="classFrame">ModificationFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html" TARGET="classFrame"><I>ModificationSetFactoryInterface</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/Module.html" TARGET="classFrame">Module</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleContext.html" TARGET="classFrame">ModuleContext</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleException.html" TARGET="classFrame">ModuleException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html" TARGET="classFrame">ModuleExceptionType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html" TARGET="classFrame"><I>ModuleFactoryInstance</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html" TARGET="classFrame"><I>ModuleIdentifier</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html" TARGET="classFrame">ModuleIdentifierList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleList.html" TARGET="classFrame">ModuleList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html" TARGET="classFrame">ModuleStorageStructure</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html" TARGET="classFrame">MotProteinParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html" TARGET="classFrame">MultiplexerFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html" TARGET="classFrame"><I>MutableSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html" TARGET="classFrame">NamedAlignmentSelectionModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html" TARGET="classFrame">NarrowedInputStream</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html" TARGET="classFrame">NoGapAtThisPositionException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html" TARGET="classFrame">NoIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html" TARGET="classFrame">NoSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html" TARGET="classFrame">NoSuchModificationException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html" TARGET="classFrame">NoSuchRequiredModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html" TARGET="classFrame">NoSuchSequenceElementException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html" TARGET="classFrame">NoSuchSequenceException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/NucleotideResidue.html" TARGET="classFrame"><I>NucleotideResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html" TARGET="classFrame">NullAlignmentSelectionModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html" TARGET="classFrame">NullColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/NullDebug.html" TARGET="classFrame">NullDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html" TARGET="classFrame">NullModuleFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html" TARGET="classFrame">NullOptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html" TARGET="classFrame">NullParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html" TARGET="classFrame"><I>Optionable</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html" TARGET="classFrame"><I>OptionableExceptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html" TARGET="classFrame">OptionableJFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html" TARGET="classFrame">OptionableJSplitPane</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html" TARGET="classFrame">OptionableSourceNotFoundException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html" TARGET="classFrame">OptionableStateException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html" TARGET="classFrame"><I>OptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html" TARGET="classFrame">PackageResourceAdapter</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/ParserException.html" TARGET="classFrame">ParserException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html" TARGET="classFrame"><I>ParserExceptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html" TARGET="classFrame">PasswordDialog</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html" TARGET="classFrame">PedanticColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html" TARGET="classFrame">PercentageIDCalculator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html" TARGET="classFrame">PercentageIDCalculatorManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html" TARGET="classFrame">PercentageIDConsensus</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html" TARGET="classFrame">PercentageIDConsensusCalculatorMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html" TARGET="classFrame">PercentageIDVarianceColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html" TARGET="classFrame">PercentIDVarianceColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html" TARGET="classFrame">PIRProteinAlignmentParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html" TARGET="classFrame">PopUpHtmlDisplay</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html" TARGET="classFrame">PrintableAlignmentPanel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html" TARGET="classFrame">PrintableJAlignmentViewer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/ProteinResidue.html" TARGET="classFrame"><I>ProteinResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html" TARGET="classFrame">ProteinSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html" TARGET="classFrame">ReaderSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html" TARGET="classFrame">ReadonlyException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Residue.html" TARGET="classFrame"><I>Residue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html" TARGET="classFrame">ResourceAdapter</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html" TARGET="classFrame">RNANucleotide</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/RNAResidue.html" TARGET="classFrame"><I>RNAResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html" TARGET="classFrame">RNASequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html" TARGET="classFrame">SaveableOptions</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Sequence.html" TARGET="classFrame"><I>Sequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html" TARGET="classFrame"><I>SequenceAlignment</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html" TARGET="classFrame">SequenceAlignmentDimension</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html" TARGET="classFrame">SequenceAlignmentPoint</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html" TARGET="classFrame">SequenceAlignmentRectangle</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html" TARGET="classFrame"><I>SequenceAlignmentShape</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html" TARGET="classFrame">SequenceAlignmentTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html" TARGET="classFrame">SequenceAlignmentToChangeableAdaptor</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html" TARGET="classFrame">SequenceCharacterIterator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html" TARGET="classFrame">SequenceColumnTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html" TARGET="classFrame"><I>SequenceCursor</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html" TARGET="classFrame">SequenceEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html" TARGET="classFrame"><I>SequenceEventProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html" TARGET="classFrame">SequenceEventType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceException.html" TARGET="classFrame">SequenceException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html" TARGET="classFrame">SequenceFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html" TARGET="classFrame">SequenceFactoryTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html" TARGET="classFrame"><I>SequenceGroup</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html" TARGET="classFrame">SequenceInputModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html" TARGET="classFrame"><I>SequenceInputParser</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html" TARGET="classFrame"><I>SequenceListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html" TARGET="classFrame">SequenceListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html" TARGET="classFrame">SequenceOutputModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html" TARGET="classFrame"><I>SequenceRetriever</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Sequences.html" TARGET="classFrame">Sequences</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html" TARGET="classFrame">SequenceSearch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html" TARGET="classFrame"><I>SequenceSource</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html" TARGET="classFrame">SequencesTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html" TARGET="classFrame"><I>SequenceType</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html" TARGET="classFrame">SequenceVetoException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html" TARGET="classFrame">SequenceWriterException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html" TARGET="classFrame">SimpleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html" TARGET="classFrame">SimpleSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html" TARGET="classFrame">SingleAlignmentSelectionModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html" TARGET="classFrame">SingleColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html" TARGET="classFrame">SingleSelectionModelTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html" TARGET="classFrame">SingleSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/SingletonModification.html" TARGET="classFrame">SingletonModification</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html" TARGET="classFrame">SliderExample</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html" TARGET="classFrame"><I>Source</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html" TARGET="classFrame">StreamSequenceSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html" TARGET="classFrame">SwappingListBasicUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html" TARGET="classFrame">SwissProtIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html" TARGET="classFrame">SystemEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html" TARGET="classFrame">SystemEventOption</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html" TARGET="classFrame"><I>SystemEventProducer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html" TARGET="classFrame">SystemEventSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html" TARGET="classFrame"><I>SystemListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html" TARGET="classFrame">SystemVetoException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html" TARGET="classFrame">TaylorColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html" TARGET="classFrame">TextFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html" TARGET="classFrame"><I>ThreadableColorMap</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html" TARGET="classFrame">ThreadedColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html" TARGET="classFrame">ThreadedConsensusSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html" TARGET="classFrame">ThreadedPercentageIDConsensusCalculatorMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html" TARGET="classFrame">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html" TARGET="classFrame">TripletPanel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html" TARGET="classFrame">UnknownElementException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html" TARGET="classFrame">URLSequenceSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html" TARGET="classFrame">ValidatedForm</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html" TARGET="classFrame">VariableColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html" TARGET="classFrame">VariationsColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html" TARGET="classFrame">VersionInformation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html" TARGET="classFrame">VetoableAlignmentEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html" TARGET="classFrame"><I>VetoableAlignmentListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html" TARGET="classFrame">VetoableSequenceEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html" TARGET="classFrame"><I>VetoableSequenceListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html" TARGET="classFrame">WeakModificationSetFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html" TARGET="classFrame">WhiteColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html" TARGET="classFrame">WholeNumberField</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html" TARGET="classFrame">XMLBootIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html" TARGET="classFrame">XMLBootModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html" TARGET="classFrame">XMLBootParserListener</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html" TARGET="classFrame">XMLLoadingTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html" TARGET="classFrame">XMLModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html" TARGET="classFrame"><I>XMLParserFactory</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html" TARGET="classFrame">XMLStartTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/Y.html" TARGET="classFrame">Y</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html" TARGET="classFrame">ZenecaColorMapMetaData</A>
+<BR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/allclasses-noframe.html b/doc/javadoc/allclasses-noframe.html
new file mode 100644
index 0000000..cfa2eaf
--- /dev/null
+++ b/doc/javadoc/allclasses-noframe.html
@@ -0,0 +1,777 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:07 BST 2002 -->
+<TITLE>
+All Classes
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="All Classes";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameHeadingFont">
+<B>All Classes</B></FONT>
+<BR>
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html" TARGET="">AbstractComplexSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html" TARGET="">AbstractComplexSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html" TARGET="">AbstractDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html" TARGET="">AbstractEditableSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html" TARGET="">AbstractElement</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html" TARGET="">AbstractEnumeratedModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html" TARGET="">AbstractEnumeratedSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html" TARGET="">AbstractEnumeration</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html" TARGET="">AbstractEnumeration.ElementIterator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html" TARGET="">AbstractGappedSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html" TARGET="">AbstractGappedSequenceGroup</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html" TARGET="">AbstractIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html" TARGET="">AbstractMutableSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html" TARGET="">AbstractProteinAlignmentInputParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html" TARGET="">AbstractProteinSequenceInputParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html" TARGET="">AbstractSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html" TARGET="">AbstractSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html" TARGET="">AbstractSequenceInput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html" TARGET="">AbstractSequenceInputParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html" TARGET="">AbstractSequenceOutput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html" TARGET="">AbstractSequenceParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html" TARGET="">AbstractSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html" TARGET="">AlignmentColumn</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html" TARGET="">AlignmentEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html" TARGET=""><I>AlignmentEventProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html" TARGET="">AlignmentEventType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html" TARGET=""><I>AlignmentInputParser</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html" TARGET=""><I>AlignmentListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html" TARGET="">AlignmentListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html" TARGET=""><I>AlignmentOutputParser</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html" TARGET="">AlignmentParserInputTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html" TARGET="">AlignmentParserIOTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html" TARGET="">AlignmentRulerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html" TARGET="">AlignmentSelectionEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html" TARGET=""><I>AlignmentSelectionListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html" TARGET="">AlignmentSelectionListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html" TARGET=""><I>AlignmentSelectionModel</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html" TARGET=""><I>AlignmentSelectionRenderer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html" TARGET="">AlignmentToListCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html" TARGET="">AlignmentToListModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html" TARGET="">AlignmentVetoException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html" TARGET=""><I>AlignmentViewerCellRenderer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html" TARGET="">AlignmentViewerTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html" TARGET="">AlignmentViewerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html" TARGET="">AminoAcid</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html" TARGET="">AminoAcidColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html" TARGET="">AnonInvoker</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html" TARGET="">ApplicationFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html" TARGET="">ArrayManipulation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html" TARGET="">BasicAlignmentRulerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html" TARGET="">BasicAlignmentViewerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html" TARGET="">BasicWindowMonitor</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html" TARGET="">BorderFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html" TARGET="">ButtonPanelTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html" TARGET="">ButtonViewerPopupMenu</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html" TARGET="">CalculatePercentageID</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html" TARGET="">CellRendererPaneReplacement</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/Changeable.html" TARGET=""><I>Changeable</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html" TARGET="">ChangeableEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ChangeableListener.html" TARGET=""><I>ChangeableListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html" TARGET="">ChangeableListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html" TARGET="">ChangeListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html" TARGET="">CheckMotifLocationAgainstPrints</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html" TARGET="">ChunkyListModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html" TARGET="">Cinema</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html" TARGET=""><I>CinemaActionProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html" TARGET="">CinemaAlignmentFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html" TARGET="">CinemaAnchorManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html" TARGET="">CinemaBoot</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html" TARGET="">CinemaBootIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html" TARGET="">CinemaColorFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html" TARGET="">CinemaColorIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html" TARGET="">CinemaColorSelector</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html" TARGET="">CinemaCommandLineParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html" TARGET="">CinemaCommandLineParserIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html" TARGET="">CinemaConsensus</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html" TARGET=""><I>CinemaConsensusCalculatorMetaData</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html" TARGET="">CinemaConsensusDisplay</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html" TARGET="">CinemaConsensusIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html" TARGET="">CinemaCoreGui</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html" TARGET="">CinemaCoreIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html" TARGET="">CinemaCoreView</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html" TARGET="">CinemaDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html" TARGET="">CinemaDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html" TARGET="">CinemaFileOptionableExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html" TARGET="">CinemaFilePersist</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html" TARGET=""><I>CinemaFramedActionProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html" TARGET="">CinemaGo</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html" TARGET="">CinemaGroup</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html" TARGET="">CinemaGroupFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html" TARGET="">CinemaGroupIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html" TARGET="">CinemaGroupManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html" TARGET="">CinemaGroupModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html" TARGET="">CinemaGuiModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html" TARGET="">CinemaInvoker</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html" TARGET="">CinemaMenuBuilder</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html" TARGET="">CinemaMenuSystem</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html" TARGET="">CinemaModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html" TARGET="">CinemaModuleCoreIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html" TARGET="">CinemaModuleFactoryInstance</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html" TARGET="">CinemaMotifFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html" TARGET="">CinemaMotifIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html" TARGET="">CinemaMotifModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html" TARGET="">CinemaMultipleConsensusViewer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html" TARGET="">CinemaPersist</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html" TARGET="">CinemaProperties</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html" TARGET="">CinemaRegexp</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html" TARGET="">CinemaResizeElements</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html" TARGET="">CinemaResources</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html" TARGET="">CinemaSequenceMenu</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html" TARGET="">CinemaShared</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html" TARGET="">CinemaSharedIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html" TARGET="">CinemaSharedQuitExit</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html" TARGET="">CinemaSlaveViewerModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html" TARGET="">CinemaSplash</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html" TARGET="">CinemaStatusInformation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html" TARGET="">CinemaSystemEvents</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html" TARGET="">CinemaTestLaunch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html" TARGET="">CinemaTestModuleLaunch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html" TARGET="">CinemaUtilityIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html" TARGET="">CinemaXMLParserFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html" TARGET="">CollectionPrinter</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html" TARGET="">ColorFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html" TARGET="">ColorGenerator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html" TARGET="">ColorList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html" TARGET=""><I>ColorMap</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html" TARGET="">ColormapColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html" TARGET="">ColorMapException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html" TARGET=""><I>ColorMapMetaData</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorStore.html" TARGET="">ColorStore</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html" TARGET=""><I>ComplexEditableGappedSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html" TARGET=""><I>ComplexElement</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html" TARGET="">ComplexElementAndModificationTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html" TARGET="">ComplexElementFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html" TARGET=""><I>ComplexElementFactoryInterface</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html" TARGET=""><I>ComplexSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html" TARGET="">ComplexSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html" TARGET=""><I>ComplexSequenceType</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html" TARGET="">ConfigNode</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html" TARGET=""><I>ConsensusCalculator</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html" TARGET="">ConsensusIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html" TARGET="">ConsensusPercentageIDColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html" TARGET=""><I>ConsensusSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html" TARGET="">CursorLessFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html" TARGET="">DatabaseIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/Debug.html" TARGET="">Debug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html" TARGET=""><I>DebugInterface</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html" TARGET="">DebugMultiplexer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html" TARGET="">DecimalField</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html" TARGET="">DefaultAlignmentSelectionRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html" TARGET="">DefaultAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html" TARGET="">DefaultColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html" TARGET="">DefaultComplexElement</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html" TARGET="">DefaultComplexSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html" TARGET="">DefaultComplexSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html" TARGET="">DefaultConsensusSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html" TARGET="">DefaultDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html" TARGET="">DefaultEditableSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html" TARGET="">DefaultFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html" TARGET="">DefaultFileDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html" TARGET="">DefaultGappedComplexSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html" TARGET="">DefaultGappedSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html" TARGET="">DefaultGappedSequenceGroup</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html" TARGET="">DefaultModuleContext</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html" TARGET="">DefaultModuleFactoryInstance</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html" TARGET="">DefaultParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html" TARGET="">DefaultSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html" TARGET="">DefaultSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html" TARGET="">DefaultSequenceCursor</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html" TARGET="">DefaultXMLParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/Direction.html" TARGET="">Direction</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html" TARGET="">DNANucleotide</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/DNAResidue.html" TARGET=""><I>DNAResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html" TARGET="">DNASequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html" TARGET="">DoubleArrayColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html" TARGET=""><I>EditableSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html" TARGET="">EditableSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Element.html" TARGET=""><I>Element</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html" TARGET="">EmptyGappedSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html" TARGET="">EmptySequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html" TARGET="">EmptySequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html" TARGET="">EmptySequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html" TARGET=""><I>ExceptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html" TARGET="">ExpasySequenceRetriever</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html" TARGET=""><I>FastAlignmentViewerCellRenderer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html" TARGET="">FastaSequenceParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html" TARGET="">FetchSequenceBySwissProtID</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html" TARGET="">FileSaveableOptions</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html" TARGET="">FileSequenceInput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html" TARGET="">FileSequenceInputParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html" TARGET="">FileSequenceOutput</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html" TARGET="">FileSequenceParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html" TARGET="">FileSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html" TARGET="">FormattedDocument</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html" TARGET="">Gap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html" TARGET="">GappableSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html" TARGET=""><I>GappedComplexSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html" TARGET=""><I>GappedSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html" TARGET="">GappedSequenceCharacterIterator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html" TARGET=""><I>GappedSequenceGroup</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html" TARGET="">GappedSequenceSearch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html" TARGET="">GappedSequenceTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html" TARGET="">GenericModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html" TARGET="">GrayScaleVariance</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html" TARGET="">GroupSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html" TARGET="">HardModificationSetFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html" TARGET=""><I>Identifiable</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html" TARGET=""><I>Identifier</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html" TARGET="">IllegalDuplicateModificationException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html" TARGET="">IndividualElementColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html" TARGET="">Install</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html" TARGET="">InstancePerAlignmentColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/IntArrayList.html" TARGET="">IntArrayList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html" TARGET="">IntegerField</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html" TARGET="">IntenseColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html" TARGET="">InvalidSequenceTypeException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html" TARGET="">InvalidSequenceTypeParserException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html" TARGET="">InvertedScrollPaneLayout</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html" TARGET="">Invoker</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html" TARGET="">InvokerInternalEventQueueException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html" TARGET="">InvokerInternalQueue</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html" TARGET="">InvokerInternalQueueException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html" TARGET="">InvokerThreadManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html" TARGET="">JAlignmentButtonPanel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html" TARGET="">JAlignmentRuler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html" TARGET="">JAlignmentViewer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html" TARGET="">JChangedScrollPane</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html" TARGET="">JLayableScrollPane</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html" TARGET="">Js_TestColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html" TARGET="">MalformedAccessionException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html" TARGET="">MetalAlignmentViewerUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html" TARGET="">Methylation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html" TARGET=""><I>Modification</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html" TARGET="">ModificationFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html" TARGET=""><I>ModificationSetFactoryInterface</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/Module.html" TARGET="">Module</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleContext.html" TARGET="">ModuleContext</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleException.html" TARGET="">ModuleException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html" TARGET="">ModuleExceptionType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html" TARGET=""><I>ModuleFactoryInstance</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html" TARGET=""><I>ModuleIdentifier</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html" TARGET="">ModuleIdentifierList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleList.html" TARGET="">ModuleList</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html" TARGET="">ModuleStorageStructure</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html" TARGET="">MotProteinParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html" TARGET="">MultiplexerFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html" TARGET=""><I>MutableSequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html" TARGET="">NamedAlignmentSelectionModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html" TARGET="">NarrowedInputStream</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html" TARGET="">NoGapAtThisPositionException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html" TARGET="">NoIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html" TARGET="">NoSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html" TARGET="">NoSuchModificationException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html" TARGET="">NoSuchRequiredModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html" TARGET="">NoSuchSequenceElementException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html" TARGET="">NoSuchSequenceException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/NucleotideResidue.html" TARGET=""><I>NucleotideResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html" TARGET="">NullAlignmentSelectionModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html" TARGET="">NullColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/debug/NullDebug.html" TARGET="">NullDebug</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html" TARGET="">NullModuleFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html" TARGET="">NullOptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html" TARGET="">NullParserExceptionHandler</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html" TARGET=""><I>Optionable</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html" TARGET=""><I>OptionableExceptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html" TARGET="">OptionableJFrame</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html" TARGET="">OptionableJSplitPane</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html" TARGET="">OptionableSourceNotFoundException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html" TARGET="">OptionableStateException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html" TARGET=""><I>OptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html" TARGET="">PackageResourceAdapter</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/ParserException.html" TARGET="">ParserException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html" TARGET=""><I>ParserExceptionHandler</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html" TARGET="">PasswordDialog</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html" TARGET="">PedanticColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html" TARGET="">PercentageIDCalculator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html" TARGET="">PercentageIDCalculatorManager</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html" TARGET="">PercentageIDConsensus</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html" TARGET="">PercentageIDConsensusCalculatorMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html" TARGET="">PercentageIDVarianceColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html" TARGET="">PercentIDVarianceColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html" TARGET="">PIRProteinAlignmentParser</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html" TARGET="">PopUpHtmlDisplay</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html" TARGET="">PrintableAlignmentPanel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html" TARGET="">PrintableJAlignmentViewer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/ProteinResidue.html" TARGET=""><I>ProteinResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html" TARGET="">ProteinSequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html" TARGET="">ReaderSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html" TARGET="">ReadonlyException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Residue.html" TARGET=""><I>Residue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html" TARGET="">ResourceAdapter</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html" TARGET="">RNANucleotide</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/RNAResidue.html" TARGET=""><I>RNAResidue</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html" TARGET="">RNASequenceType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html" TARGET="">SaveableOptions</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Sequence.html" TARGET=""><I>Sequence</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html" TARGET=""><I>SequenceAlignment</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html" TARGET="">SequenceAlignmentDimension</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html" TARGET="">SequenceAlignmentPoint</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html" TARGET="">SequenceAlignmentRectangle</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html" TARGET=""><I>SequenceAlignmentShape</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html" TARGET="">SequenceAlignmentTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html" TARGET="">SequenceAlignmentToChangeableAdaptor</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html" TARGET="">SequenceCharacterIterator</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html" TARGET="">SequenceColumnTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html" TARGET=""><I>SequenceCursor</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html" TARGET="">SequenceEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html" TARGET=""><I>SequenceEventProvider</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html" TARGET="">SequenceEventType</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceException.html" TARGET="">SequenceException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html" TARGET="">SequenceFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html" TARGET="">SequenceFactoryTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html" TARGET=""><I>SequenceGroup</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html" TARGET="">SequenceInputModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html" TARGET=""><I>SequenceInputParser</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html" TARGET=""><I>SequenceListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html" TARGET="">SequenceListenerSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html" TARGET="">SequenceOutputModuleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html" TARGET=""><I>SequenceRetriever</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/Sequences.html" TARGET="">Sequences</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html" TARGET="">SequenceSearch</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html" TARGET=""><I>SequenceSource</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html" TARGET="">SequencesTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html" TARGET=""><I>SequenceType</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html" TARGET="">SequenceVetoException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html" TARGET="">SequenceWriterException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html" TARGET="">SimpleIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html" TARGET="">SimpleSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html" TARGET="">SingleAlignmentSelectionModel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html" TARGET="">SingleColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html" TARGET="">SingleSelectionModelTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html" TARGET="">SingleSequenceAlignment</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/SingletonModification.html" TARGET="">SingletonModification</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html" TARGET="">SliderExample</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html" TARGET=""><I>Source</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html" TARGET="">StreamSequenceSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html" TARGET="">SwappingListBasicUI</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html" TARGET="">SwissProtIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html" TARGET="">SystemEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html" TARGET="">SystemEventOption</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html" TARGET=""><I>SystemEventProducer</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html" TARGET="">SystemEventSupport</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html" TARGET=""><I>SystemListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html" TARGET="">SystemVetoException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html" TARGET="">TaylorColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html" TARGET="">TextFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html" TARGET=""><I>ThreadableColorMap</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html" TARGET="">ThreadedColorMap</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html" TARGET="">ThreadedConsensusSequence</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html" TARGET="">ThreadedPercentageIDConsensusCalculatorMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html" TARGET="">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html" TARGET="">TripletPanel</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html" TARGET="">UnknownElementException</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html" TARGET="">URLSequenceSource</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html" TARGET="">ValidatedForm</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html" TARGET="">VariableColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html" TARGET="">VariationsColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html" TARGET="">VersionInformation</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html" TARGET="">VetoableAlignmentEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html" TARGET=""><I>VetoableAlignmentListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html" TARGET="">VetoableSequenceEvent</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html" TARGET=""><I>VetoableSequenceListener</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html" TARGET="">WeakModificationSetFactory</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html" TARGET="">WhiteColorMapMetaData</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html" TARGET="">WholeNumberField</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html" TARGET="">XMLBootIdentifier</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html" TARGET="">XMLBootModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html" TARGET="">XMLBootParserListener</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html" TARGET="">XMLLoadingTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html" TARGET="">XMLModule</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html" TARGET=""><I>XMLParserFactory</I></A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html" TARGET="">XMLStartTest</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/Y.html" TARGET="">Y</A>
+<BR>
+<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html" TARGET="">ZenecaColorMapMetaData</A>
+<BR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/constant-values.html b/doc/javadoc/constant-values.html
new file mode 100644
index 0000000..9189ca9
--- /dev/null
+++ b/doc/javadoc/constant-values.html
@@ -0,0 +1,519 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:11:49 BST 2002 -->
+<TITLE>
+Constant Field Values
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Constant Field Values";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="constant-values.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H1>
+Constant Field Values</H1>
+</CENTER>
+<HR SIZE="4" NOSHADE>
+<B>Contents</B><UL>
+<LI><A HREF="#uk.ac">uk.ac.*</A>
+</UL>
+
+<A NAME="uk.ac"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD ALIGN="left"><FONT SIZE="+2">
+<B>uk.ac.*</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Percentage ID Consensus Calculator"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Amino Acid Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Colormap Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Default Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Intense Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Js_Test Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Pedantic Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Taylor Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Variable Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Variations Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Zeneca Color Scheme"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager.groupsName"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#groupsName">groupsName</A></CODE></TD>
+<TD ALIGN="right"><CODE>"groups"</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager.groupsOrder"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#groupsOrder">groupsOrder</A></CODE></TD>
+<TD ALIGN="right"><CODE>"order"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.debug.Debug.debug"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final boolean</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/debug/Debug.html#debug">debug</A></CODE></TD>
+<TD ALIGN="right"><CODE>0</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Percentage ID variance Color Map"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.color.ThreadedColorMap.NAME"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#NAME">NAME</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Threaded Color Map"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.util.forms.ValidatedForm.EQUALS"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#EQUALS">EQUALS</A></CODE></TD>
+<TD ALIGN="right"><CODE>2</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.util.forms.ValidatedForm.GREATER_THAN"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#GREATER_THAN">GREATER_THAN</A></CODE></TD>
+<TD ALIGN="right"><CODE>1</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.util.forms.ValidatedForm.LESS_THAN"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#LESS_THAN">LESS_THAN</A></CODE></TD>
+<TD ALIGN="right"><CODE>0</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.util.forms.ValidatedForm.LIKE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#LIKE">LIKE</A></CODE></TD>
+<TD ALIGN="right"><CODE>3</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.viewer.JAlignmentRuler.uiClassID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#uiClassID">uiClassID</A></CODE></TD>
+<TD ALIGN="right"><CODE>"AlignmentRulerUI"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.viewer.JAlignmentViewer.uiClassID"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#uiClassID">uiClassID</A></CODE></TD>
+<TD ALIGN="right"><CODE>"AlignmentViewerUI"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=3><B>uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.DOWN"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#DOWN">DOWN</A></CODE></TD>
+<TD ALIGN="right"><CODE>2</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.LEFT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#LEFT">LEFT</A></CODE></TD>
+<TD ALIGN="right"><CODE>4</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.RIGHT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#RIGHT">RIGHT</A></CODE></TD>
+<TD ALIGN="right"><CODE>3</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.UP"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public static final int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#UP">UP</A></CODE></TD>
+<TD ALIGN="right"><CODE>1</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="constant-values.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/deprecated-list.html b/doc/javadoc/deprecated-list.html
new file mode 100644
index 0000000..7626fd9
--- /dev/null
+++ b/doc/javadoc/deprecated-list.html
@@ -0,0 +1,121 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:07 BST 2002 -->
+<TITLE>
+Deprecated List ()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Deprecated List ()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="deprecated-list.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+<B>Deprecated API</B></H2>
+</CENTER>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Deprecated</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="deprecated-list.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/help-doc.html b/doc/javadoc/help-doc.html
new file mode 100644
index 0000000..1160bd9
--- /dev/null
+++ b/doc/javadoc/help-doc.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:40 BST 2002 -->
+<TITLE>
+API Help ()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="API Help ()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="help-doc.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H1>
+How This API Document Is Organized</H1>
+</CENTER>
+This API (Application Programming Interface) document has pages corresponding to the items in the navigation bar, described as follows.<H3>
+Overview</H3>
+<BLOCKQUOTE>
+
+<P>
+The <A HREF="overview-summary.html">Overview</A> page is the front page of this API document and provides a list of all packages with a summary for each. This page can also contain an overall description of the set of packages.</BLOCKQUOTE>
+<H3>
+Package</H3>
+<BLOCKQUOTE>
+
+<P>
+Each package has a page that contains a list of its classes and interfaces, with a summary for each. This page can contain four categories:<UL>
+<LI>Interfaces (italic)<LI>Classes<LI>Exceptions<LI>Errors</UL>
+</BLOCKQUOTE>
+<H3>
+Class/Interface</H3>
+<BLOCKQUOTE>
+
+<P>
+Each class, interface, nested class and nested interface has its own separate page. Each of these pages has three sections consisting of a class/interface description, summary tables, and detailed member descriptions:<UL>
+<LI>Class inheritance diagram<LI>Direct Subclasses<LI>All Known Subinterfaces<LI>All Known Implementing Classes<LI>Class/interface declaration<LI>Class/interface description
+<P>
+<LI>Nested Class Summary<LI>Field Summary<LI>Constructor Summary<LI>Method Summary
+<P>
+<LI>Field Detail<LI>Constructor Detail<LI>Method Detail</UL>
+Each summary entry contains the first sentence from the detailed description for that item. The summary entries are alphabetical, while the detailed descriptions are in the order they appear in the source code. This preserves the logical groupings established by the programmer.</BLOCKQUOTE>
+<H3>
+Tree (Class Hierarchy)</H3>
+<BLOCKQUOTE>
+There is a <A HREF="overview-tree.html">Class Hierarchy</A> page for all packages, plus a hierarchy for each package. Each hierarchy page contains a list of classes and a list of interfaces. The classes are organized by inheritance structure starting with <code>java.lang.Object</code>. The interfaces do not inherit from <code>java.lang.Object</code>.<UL>
+<LI>When viewing the Overview page, clicking on "Tree" displays the hierarchy for all packages.<LI>When viewing a particular package, class or interface page, clicking "Tree" displays the hierarchy for only that package.</UL>
+</BLOCKQUOTE>
+<H3>
+Deprecated API</H3>
+<BLOCKQUOTE>
+The <A HREF="deprecated-list.html">Deprecated API</A> page lists all of the API that have been deprecated. A deprecated API is not recommended for use, generally due to improvements, and a replacement API is usually given. Deprecated APIs may be removed in future implementations.</BLOCKQUOTE>
+<H3>
+Index</H3>
+<BLOCKQUOTE>
+The <A HREF="index-all.html">Index</A> contains an alphabetic list of all classes, interfaces, constructors, methods, and fields.</BLOCKQUOTE>
+<H3>
+Prev/Next</H3>
+These links take you to the next or previous class, interface, package, or related page.<H3>
+Frames/No Frames</H3>
+These links show and hide the HTML frames. All pages are available with or without frames.
+<P>
+<H3>
+Serialized Form</H3>
+Each serializable or externalizable class has a description of its serialization fields and methods. This information is of interest to re-implementors, not to developers using the API. While there is no link in the navigation bar, you can get to this information by going to any serialized class and clicking "Serialized Form" in the "See also" section of the class description.
+<P>
+<FONT SIZE="-1">
+<EM>
+This help file applies to API documentation generated using the standard doclet.</EM>
+</FONT>
+<BR>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Help</B></FONT> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="help-doc.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/index-all.html b/doc/javadoc/index-all.html
new file mode 100644
index 0000000..01f8c31
--- /dev/null
+++ b/doc/javadoc/index-all.html
@@ -0,0 +1,8309 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:11:54 BST 2002 -->
+<TITLE>
+Index ()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Index ()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="index-all.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_J_">J</A> <A HREF="#_K_">K</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <A HREF="#_X_">X</A> <A HREF=" [...]
+<A NAME="_A_"><!-- --></A><H2>
+<B>A</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html#aa"><B>aa</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html"><B>AbstractComplexSequence</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>.<DD>AbstractComplexSequence.java
+
+
+ Created: Fri Nov 24 13:33:32 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#AbstractComplexSequence(uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)"><B>AbstractComplexSequence(ComplexSequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>AbstractComplexSequenceType</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>.<DD>AbstractComplexSequenceType.java
+
+
+ Created: Tue Feb 29 22:10:30 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#AbstractComplexSequenceType(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification[], java.lang.String)"><B>AbstractComplexSequenceType(Residue[], Modification[], String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#AbstractComplexSequenceType(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification, java.lang.String)"><B>AbstractComplexSequenceType(Residue[], Modification, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html"><B>AbstractDebug</B></A> - class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>.<DD>AbstractDebug.java
+
+
+ Created: Wed Mar 1 22:22:22 2000<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#AbstractDebug()"><B>AbstractDebug()</B></A> -
+Constructor for class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html"><B>AbstractEditableSequence</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>.<DD>AbstractEditableSequence.java
+
+ This class provides trivial implementations of all of those methods
+ which can be defined in terms of the others of the EditableSequence
+ interface, and also ensures that the event handling occurs correctly
+
+ Created: Fri Mar 3 12:11:49 2000<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#AbstractEditableSequence(uk.ac.man.bioinf.sequence.SequenceType)"><B>AbstractEditableSequence(SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html"><B>AbstractElement</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A>.<DD>AbstractElement.java
+
+
+ Created: Mon Feb 28 16:10:45 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html#AbstractElement(java.lang.String, char)"><B>AbstractElement(String, char)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>.<DD>AbstractEnumeratedModuleIdentifier.java
+
+
+ Created: Sun May 7 17:42:13 2000<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#AbstractEnumeratedModuleIdentifier(java.lang.String, java.lang.String)"><B>AbstractEnumeratedModuleIdentifier(String, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#AbstractEnumeratedModuleIdentifier(java.lang.String, java.lang.String, boolean)"><B>AbstractEnumeratedModuleIdentifier(String, String, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>AbstractEnumeratedSequenceType</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A>.<DD>AbstractEnumeratedSequenceType.java
+
+
+ Created: Tue Jun 13 13:20:11 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#AbstractEnumeratedSequenceType(uk.ac.man.bioinf.sequence.Element[][], java.lang.String)"><B>AbstractEnumeratedSequenceType(Element[][], String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#AbstractEnumeratedSequenceType(uk.ac.man.bioinf.sequence.Element[], java.lang.String)"><B>AbstractEnumeratedSequenceType(Element[], String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>.<DD>AbstractEnumeration.java
+
+ Provides support for Enumerated Types in Java.<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>AbstractEnumeration.ElementIterator</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#AbstractEnumeration.ElementIterator(java.lang.Class)"><B>AbstractEnumeration.ElementIterator [...]
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html#AbstractEnumeration(java.lang.String)"><B>AbstractEnumeration(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html"><B>AbstractGappedSequence</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>.<DD>AbstractGappedSequence.java
+
+
+ Created: Sat Mar 4 12:17:02 2000<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#AbstractGappedSequence(uk.ac.man.bioinf.sequence.SequenceType)"><B>AbstractGappedSequence(SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html"><B>AbstractGappedSequenceGroup</B></A> - class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A>.<DD>AbstractGappedSequenceGroup.java
+
+
+ Created: Thu Jun 1 18:25:15 2000<DT><A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#AbstractGappedSequenceGroup()"><B>AbstractGappedSequenceGroup()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html"><B>AbstractIdentifier</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A>.<DD>AbstractSequenceIdentifier.java
+
+
+ Created: Wed Jul 5 16:00:43 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#AbstractIdentifier(uk.ac.man.bioinf.sequence.identifier.Source)"><B>AbstractIdentifier(Source)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>AbstractMutableSequence</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>.<DD>AbstractMutableSequence.java
+
+
+ Created: Thu Mar 2 20:20:02 2000<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#AbstractMutableSequence(uk.ac.man.bioinf.sequence.SequenceType)"><B>AbstractMutableSequence(SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html"><B>AbstractProteinAlignmentInputParser</B></A> - class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A>.<DD>Provides a function to parse amino acids from the input stream.<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html#AbstractProteinAlignmentInputParser()"><B>AbstractProteinA [...]
+Constructor for class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>AbstractProteinSequenceInputParser</B></A> - class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A>.<DD>AbstractProteinSequenceInputParser.java
+
+ Provides a root class for all protein sequence parsers.<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#AbstractProteinSequenceInputParser()"><B>AbstractProteinSequenceInputParser()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>AbstractSequence</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>.<DD>AbstractSequence.java
+
+ Provides some of the methods for sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#AbstractSequence(uk.ac.man.bioinf.sequence.SequenceType)"><B>AbstractSequence(SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>AbstractSequenceAlignment</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>.<DD>AbstractSequenceAlignment.java
+
+ An abstract class to extend for the basic definition of a multiple
+ sequence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#AbstractSequenceAlignment()"><B>AbstractSequenceAlignment()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html"><B>AbstractSequenceInput</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>.<DD>This class is abstract and will be extended by any sequence input
+ modules.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#AbstractSequenceInput()"><B>AbstractSequenceInput()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>AbstractSequenceInputParserExceptionHandler</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A>.<DD>AbstractSequenceInputParserExceptionHandler provides methods so
+ that the exceptions can be stored and at a later date shown all
+ together.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#AbstractSequenceInputParserExceptionHandler()"><B>AbstractSequenceInputParserExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>AbstractSequenceOutput</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>.<DD>This class is abstract and will be extended by any sequence output
+ modules.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#AbstractSequenceOutput()"><B>AbstractSequenceOutput()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>AbstractSequenceParserExceptionHandler</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A>.<DD>AbstractSequenceInputParserExceptionHandler provides methods so
+ that the exceptions can be stored and at a later date shown all
+ together.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#AbstractSequenceParserExceptionHandler()"><B>AbstractSequenceParserExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>AbstractSequenceType</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>.<DD>AbstractSequenceType.java
+
+
+ Created: Thu Feb 17 13:02:28 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#AbstractSequenceType(uk.ac.man.bioinf.sequence.Element[][], java.lang.String)"><B>AbstractSequenceType(Element[][], String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#AbstractSequenceType(uk.ac.man.bioinf.sequence.Element[], java.lang.String)"><B>AbstractSequenceType(Element[], String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html">BasicAlignmentViewerUI.SelectionClearer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html">BasicAlignmentViewerUI.SelectionToggler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#actionPerformed(java.awt.event.ActionEvent)"><B>actionPerformed(ActionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#add(int)"><B>add(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#add(int, int)"><B>add(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#add(int, int)"><B>add(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#add(int, java.lang.Object)"><B>add(int, Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#add(javax.swing.JMenuItem)"><B>add(JMenuItem)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#add(uk.ac.man.bioinf.module.Module)"><B>add(Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Adds a module to the list.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#add(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>add(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Adds a module identifier to the list.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#add(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>add(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Delegates to the AlignmentListenerSupport object, the addition
+ of a Multiple Sequence (MS) listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>Adds a alignment listener to a Vector of listeners.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>
+<DD>Add a listener specifically interested in events connected with the MSA.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>addAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>addAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>addAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>addAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>addAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>addAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html">AlignmentSelectionListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addAll(java.util.Collection)"><B>addAll(Collection)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>This method takes a collection, adds all the elements,
+ then fires an event.
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addAll(java.lang.Object[])"><B>addAll(Object[])</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>Add all the elements of this array to the list model
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addAll(java.util.Vector)"><B>addAll(Vector)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>Add all the elements of this vector to the list model
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addButton(java.lang.String)"><B>addButton(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a button with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addButton(java.lang.String, java.lang.String)"><B>addButton(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a button with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addButton(java.lang.String, java.lang.String, java.lang.String)"><B>addButton(String, String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a button with the specified text label, icon and tooltip.
+<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html#addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><B>addChangeListener(ChangeableListener)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/Changeable.html#addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><B>addChangeListener(ChangeableListener)</B></A> -
+Method in interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Changeable.html">Changeable</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#addChangeListener(javax.swing.event.ChangeListener)"><B>addChangeListener(ChangeListener)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>
+<DD>Add a listener to this cursor
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#addChangeListener(javax.swing.event.ChangeListener)"><B>addChangeListener(ChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#addChangeListener(javax.swing.event.ChangeListener)"><B>addChangeListener(ChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html">ChangeListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#addChildNode(uk.ac.man.bioinf.apps.xml.ConfigNode)"><B>addChildNode(ConfigNode)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)"><B>addCinemaPropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><B>addCinemaPropertyChangeListener(String, PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement[], uk.ac.man.bioinf.sequence.complex.Modification[])"><B>addComplexElement(ComplexElement[], Modification[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><B>addComplexElement(ComplexElement, Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><B>addComplexElement(ComplexElement, Modification)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification[])"><B>addComplexElement(Residue[], Modification[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#addComplexElement(uk.ac.man.bioinf.sequence.Residue, uk.ac.man.bioinf.sequence.complex.Modification)"><B>addComplexElement(Residue, Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.Residue, uk.ac.man.bioinf.sequence.complex.Modification)"><B>addComplexElement(Residue, Modification)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><B>addConfig(ModuleIdentifier, Object)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><B>addConfig(ModuleIdentifier, Object)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#addConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><B>addConsensusSequence(ConsensusSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#addCursorChangeListener(javax.swing.event.ChangeListener)"><B>addCursorChangeListener(ChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#addDebugInstance(uk.ac.man.bioinf.debug.DebugInterface)"><B>addDebugInstance(DebugInterface)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>Add a new Debug Interface instance.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addDecimalField(java.lang.String, java.lang.String, boolean, int, boolean)"><B>addDecimalField(String, String, boolean, int, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addDecimalField(java.lang.String, java.lang.String, double, boolean, int, boolean)"><B>addDecimalField(String, String, double, boolean, int, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addElement(java.lang.Object)"><B>addElement(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>addIdentifier(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>addIdentifier(ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Adds an identifier to the factory storage mechanism.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>addIdentifier(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])"><B>addIdentifier(ModuleIdentifier[])</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])"><B>addIdentifier(ModuleIdentifier[])</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Adds identifiers to the factory storage mechanism.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])"><B>addIdentifier(ModuleIdentifier[])</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addIntegerField(java.lang.String, java.lang.String, boolean, int)"><B>addIntegerField(String, String, boolean, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addIntegerField(java.lang.String, java.lang.String, int, boolean, int)"><B>addIntegerField(String, String, int, boolean, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#addItemListener(java.awt.event.ItemListener)"><B>addItemListener(ItemListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#addListDataListener(javax.swing.event.ListDataListener)"><B>addListDataListener(ListDataListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">AlignmentToListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addMenu(java.lang.String)"><B>addMenu(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a menu with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addMenuItem(java.lang.String, java.lang.String)"><B>addMenuItem(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>create a menu with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#addMetaData(uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)"><B>addMetaData(ColorMapMetaData)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><B>addModificationAt(Modification, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><B>addModificationAt(Modification, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>addOptionable(Optionable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>addOptionable(Optionable)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>
+<DD>Add an optionable object.
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>addOptionable(Optionable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html">NullOptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#addPropertyChangeListener(java.beans.PropertyChangeListener)"><B>addPropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)"><B>addPropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><B>addPropertyChangeListener(String, PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><B>addPropertyChangeListener(String, PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#addRequiredModule(uk.ac.man.bioinf.module.Module)"><B>addRequiredModule(Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module)"><B>addRequiredModule(ModuleIdentifier, Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#addRequiredModules(uk.ac.man.bioinf.module.Module[])"><B>addRequiredModules(Module[])</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module[])"><B>addRequiredModules(ModuleIdentifier, Module[])</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>addSequence(GappedSequence, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Adds a sequence to the current alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>addSequence(GappedSequence, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>addSequence(GappedSequence, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Adds a sequence to the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>addSequence(GappedSequence, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>addSequence(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Calls addSequence on every sequence in the supplied
+ alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>Adds a sequence listener object to a Vector of listeners.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>addSequenceListener(SequenceListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>
+<DD>Adds the specified sequence listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>addSequenceQuietly(GappedSequence, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Adds a sequence quietly to the alignment (i.e., without notifying
+ listeners - it should really only be done from it's parent
+ procedure addSequence).
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>addSequenceQuietly(GappedSequence, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Adds a sequence to the alignment, quietly, without notifying
+ listeners.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)"><B>addSequenceToGroup(Sequence)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Adds a sequence to this group
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)"><B>addSequenceToGroup(Sequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>Adds a sequence to this group.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)"><B>addSequenceToGroup(Sequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addSubMenu(java.lang.String, java.lang.String)"><B>addSubMenu(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>create a menu with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><B>addSystemEventListener(SystemListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><B>addSystemEventListener(SystemListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><B>addSystemEventListener(SystemListener)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addTextField(java.lang.String, java.lang.String, java.lang.String, boolean, int)"><B>addTextField(String, String, String, boolean, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addToggleButton(java.lang.String)"><B>addToggleButton(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a button with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addToggleButton(java.lang.String, java.lang.String)"><B>addToggleButton(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a button with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addToggleButton(java.lang.String, java.lang.String, java.lang.String)"><B>addToggleButton(String, String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>add a button with the specified text label, icon and tooltip.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Delegates to the AlignmentListenerSupport the addition of a
+ vetoable MS listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>Adds a vetoable alignment listener to the Vector of vetoable
+ listeners.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>
+<DD>Adds a listener interested in vetoing multiple sequence alignment
+ specific events.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>addVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>Adds a vetoable sequence listener to the Vector of listeners.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>addVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>
+<DD>Adds the specified vetoable sequence listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html#ADENOSINE"><B>ADENOSINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html#ADENOSINE"><B>ADENOSINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ALANINE"><B>ALANINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>AlignmentColumn</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>.<DD>AlignmentColumn.java
+
+ The Sequence and SequenceAlignment classes have been created to be fail-fast.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#AlignmentColumn()"><B>AlignmentColumn()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#AlignmentColumn(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>AlignmentColumn(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html"><B>AlignmentEvent</B></A> - class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A>.<DD>AlignmentEvent.java
+
+ Instances of this class represent an event to a MSA.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#AlignmentEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><B>AlignmentEvent(Object, int, AlignmentEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A>
+<DD>Constructor to set the event source, location and type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#AlignmentEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><B>AlignmentEvent(Object, int, int, AlignmentEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A>
+<DD>Constructor to set the event source, location and type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html"><B>AlignmentEventProvider</B></A> - interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>.<DD>AlignmentEventProvider.java
+
+
+ Created: Mon Apr 24 16:59:55 2000<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>AlignmentEventType</B></A> - class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>.<DD>AlignmentEventType.java
+
+ This class provides an enumerated type for the AlignmentEvent class
+ to pass around as an identifier
+
+ Created: Tue Feb 15 20:26:54 2000<DT><A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html"><B>AlignmentInputParser</B></A> - interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>.<DD>This is an interface that provides a definition for any sequence
+ parsers.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>AlignmentListener</B></A> - interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>.<DD>AlignmentListener.java
+
+ Objects of this type should be signalled after a change has occured
+ to a multiple sequence alignment<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>AlignmentListenerSupport</B></A> - class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>.<DD>AlignmentListenerSupport.java
+
+ This class provides support and handles the listeners to a multiple
+ seqyence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#AlignmentListenerSupport()"><B>AlignmentListenerSupport()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>AlignmentOutputParser</B></A> - interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A>.<DD>This is an interface that provides a definition for any sequence
+ output parsing.<DT><A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html"><B>AlignmentParserInputTest</B></A> - class uk.ac.man.bioinf.io.test.<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html">AlignmentParserInputTest</A>.<DD>AlignmentParserInputTest.java
+
+
+ Created: Wed Jun 7 19:18:07 2000<DT><A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html#AlignmentParserInputTest()"><B>AlignmentParserInputTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.test.<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html">AlignmentParserInputTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html"><B>AlignmentParserIOTest</B></A> - class uk.ac.man.bioinf.io.test.<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html">AlignmentParserIOTest</A>.<DD>AlignmentParserIOTest.java
+
+
+ Created: Mon Aug 14 16:46:12 2000<DT><A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html#AlignmentParserIOTest()"><B>AlignmentParserIOTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.test.<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html">AlignmentParserIOTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html"><B>AlignmentRulerUI</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html">AlignmentRulerUI</A>.<DD>AlignmentRulerUI.java
+
+
+ Created: Thu Mar 23 17:10:05 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html#AlignmentRulerUI()"><B>AlignmentRulerUI()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html">AlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html"><B>AlignmentSelectionEvent</B></A> - class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A>.<DD>AlignmentSelectionEvent.java
+
+
+ Created: Mon Apr 10 12:22:22 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#AlignmentSelectionEvent(java.lang.Object, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle, boolean)"><B>AlignmentSelectionEvent(Object, SequenceAlignmentRectangle, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html"><B>AlignmentSelectionListener</B></A> - interface uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>.<DD>AlignmentSelectionListener.java
+
+
+ Created: Mon Apr 10 12:12:33 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html"><B>AlignmentSelectionListenerSupport</B></A> - class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html">AlignmentSelectionListenerSupport</A>.<DD>AlignmentSelectionListenerSupport.java
+
+
+ Created: Mon Apr 10 12:31:19 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#AlignmentSelectionListenerSupport()"><B>AlignmentSelectionListenerSupport()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html">AlignmentSelectionListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html"><B>AlignmentSelectionModel</B></A> - interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>.<DD>AlignmentSelectionModel.java
+
+ This defines the selection model for the JAlignmentViewer.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html"><B>AlignmentSelectionRenderer</B></A> - interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A>.<DD>SelectionRenderer.java
+
+
+ Created: Wed Mar 7 18:45:50 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html"><B>AlignmentToListCellRenderer</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html">AlignmentToListCellRenderer</A>.<DD>AlignmentToListCellRenderer.java
+
+
+ Created: Tue May 16 18:02:22 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html#AlignmentToListCellRenderer()"><B>AlignmentToListCellRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html">AlignmentToListCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>AlignmentToListModel</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">AlignmentToListModel</A>.<DD>AlignmentToListModel.java
+
+
+ Created: Tue May 16 17:55:45 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#AlignmentToListModel(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>AlignmentToListModel(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">AlignmentToListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html"><B>AlignmentVetoException</B></A> - exception uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>.<DD>AlignmentVetoExcception.java
+
+ An exception thrown when an object vetos an alignment event.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html#AlignmentVetoException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>AlignmentVetoException(String, AlignmentEvent)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>
+<DD>Constructor; includes reference to the event which spawned the veto.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html"><B>AlignmentViewerCellRenderer</B></A> - interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A>.<DD>AlignmentViewerCellRenderer.java
+
+ Initial interface for the AlignmentViewerCellRender.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html"><B>AlignmentViewerTest</B></A> - class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html">AlignmentViewerTest</A>.<DD>AlignmentViewerTest.java
+
+
+ Created: Wed Mar 15 20:11:02 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html#AlignmentViewerTest()"><B>AlignmentViewerTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html">AlignmentViewerTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>AlignmentViewerUI</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>.<DD>AlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:29:34 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#AlignmentViewerUI()"><B>AlignmentViewerUI()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>AminoAcid</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>.<DD>AminoAcid.java
+
+ A class for the representation of an amino-acid.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html"><B>AminoAcidColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>.<DD>AminoAcidColorMapMetaData.java
+
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#AminoAcidColorMapMetaData()"><B>AminoAcidColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#anchorAll()"><B>anchorAll()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#anchorGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><B>anchorGroup(CinemaGroup)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html"><B>AnonInvoker</B></A> - class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>.<DD>AnonInvoker.java
+
+ This class is used with the InvokerInternalQueue.<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#AnonInvoker()"><B>AnonInvoker()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#AnonInvoker(java.lang.Object)"><B>AnonInvoker(Object)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#AnonInvoker(java.lang.Object, java.lang.Object)"><B>AnonInvoker(Object, Object)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ANY"><B>ANY</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html"><B>ApplicationFrame</B></A> - class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>.<DD>Provides a JFrame with a menu, a tool bar, a mainwindow and a status bar.<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#ApplicationFrame()"><B>ApplicationFrame()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#ApplicationFrame(java.lang.String)"><B>ApplicationFrame(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>Create an Application frame with the resources specified.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ARGININE"><B>ARGININE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html"><B>ArrayManipulation</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html">ArrayManipulation</A>.<DD>ArrayManipulation.java
+
+ Just some utility functions for manipulating arrays.<DT><A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html#ArrayManipulation()"><B>ArrayManipulation()</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html">ArrayManipulation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ASNORASP"><B>ASNORASP</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ASPARAGINE"><B>ASPARAGINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ASPARTICACID"><B>ASPARTICACID</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#attemptSystemExit()"><B>attemptSystemExit()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_B_"><!-- --></A><H2>
+<B>B</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>BasicAlignmentRulerUI</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>.<DD>BasicAlignmentRulerUI.java
+
+
+ Created: Thu Mar 23 17:10:31 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#BasicAlignmentRulerUI(javax.swing.JComponent)"><B>BasicAlignmentRulerUI(JComponent)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>BasicAlignmentViewerUI</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>.<DD>BasicAlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:30:36 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>BasicAlignmentViewerUI.KeyScroller</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#BasicAlignmentViewerUI.KeyScroller(uk.ac.man.bioinf.gui.viewer.JAl [...]
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>BasicAlignmentViewerUI.PointListener</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html">BasicAlignmentViewerUI.PointListener</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html#BasicAlignmentViewerUI.PointListener()"><B>BasicAlignmentViewerUI.PointListener()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html">BasicAlignmentViewerUI.PointListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>BasicAlignmentViewerUI.SelectionClearer</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html">BasicAlignmentViewerUI.SelectionClearer</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html#BasicAlignmentViewerUI.SelectionClearer()"><B>BasicAlignmentViewerUI.Select [...]
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html">BasicAlignmentViewerUI.SelectionClearer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>BasicAlignmentViewerUI.SelectionToggler</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html">BasicAlignmentViewerUI.SelectionToggler</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html#BasicAlignmentViewerUI.SelectionToggler()"><B>BasicAlignmentViewerUI.Select [...]
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html">BasicAlignmentViewerUI.SelectionToggler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#BasicAlignmentViewerUI()"><B>BasicAlignmentViewerUI()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>BasicWindowMonitor</B></A> - class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html">BasicWindowMonitor</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html#BasicWindowMonitor()"><B>BasicWindowMonitor()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html">BasicWindowMonitor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#binarySearch(int)"><B>binarySearch(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>This method performs a binary search on the list.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html"><B>BorderFastAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html">BorderFastAlignmentViewerCellRenderer</A>.<DD>BorderFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html#BorderFastAlignmentViewerCellRenderer()"><B>BorderFastAlignmentViewerCellRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html">BorderFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><B>both(Class, Object, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><B>both(Class, Object, Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><B>both(Class, Object, Throwable)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><B>both(Class, Object, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)"><B>both(Class, String, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)"><B>both(Class, String, Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)"><B>both(Class, String, Throwable)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)"><B>both(Class, String, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><B>both(Object, Object, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><B>both(Object, Object, Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><B>both(Object, Object, Throwable)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><B>both(Object, Object, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)"><B>both(Object, String, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)"><B>both(Object, String, Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)"><B>both(Object, String, Throwable)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)"><B>both(Object, String, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html#buildMenu(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame, javax.swing.JMenuBar, uk.ac.man.bioinf.apps.xml.ConfigNode[])"><B>buildMenu(CinemaAlignmentFrame, JMenuBar, ConfigNode[])</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html">CinemaMenuBuilder</A>
+<DD>This is the build method.
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#bundle"><B>bundle</B></A> -
+Variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>ButtonPanelTest</B></A> - class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html">ButtonPanelTest</A>.<DD>ButtonPanelTest.java
+
+
+ Created: Fri May 19 17:22:31 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html#ButtonPanelTest()"><B>ButtonPanelTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html">ButtonPanelTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>ButtonViewerPopupMenu</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html">ButtonViewerPopupMenu</A>.<DD>ButtonViewerPopupMenu.java
+
+ This class implements a pop up menu for the
+ JAlignmentButtonPanel.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html#ButtonViewerPopupMenu(uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel)"><B>ButtonViewerPopupMenu(JAlignmentButtonPanel)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html">ButtonViewerPopupMenu</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_C_"><!-- --></A><H2>
+<B>C</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#calcConsensus()"><B>calcConsensus()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html#calculate()"><B>calculate()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#calculate()"><B>calculate()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateGeometry()"><B>calculateGeometry()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html"><B>CalculatePercentageID</B></A> - class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html">CalculatePercentageID</A>.<DD>CalculatePercentageID.java
+
+
+ Created: Tue Jan 30 17:42:44 2001<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html#CalculatePercentageID()"><B>CalculatePercentageID()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html">CalculatePercentageID</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateThumbLocation()"><B>calculateThumbLocation()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateTrackBuffer()"><B>calculateTrackBuffer()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateTrackRect()"><B>calculateTrackRect()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#calculateViableRenderers(int)"><B>calculateViableRenderers(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#capacity()"><B>capacity()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>CellRendererPaneReplacement</B></A> - class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html">CellRendererPaneReplacement</A>.<DD>CellRendererPaneReplacement.java
+
+
+ Created: Fri Apr 14 17:02:05 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html#CellRendererPaneReplacement()"><B>CellRendererPaneReplacement()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html">CellRendererPaneReplacement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/Changeable.html"><B>Changeable</B></A> - interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Changeable.html">Changeable</A>.<DD>Changeable.java
+
+
+ Created: Wed Jul 19 17:26:01 2000<DT><A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html"><B>ChangeableEvent</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html">ChangeableEvent</A>.<DD>ChangeableEvent.java
+
+
+ Created: Wed Jul 19 17:29:43 2000<DT><A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html#ChangeableEvent(java.lang.Object)"><B>ChangeableEvent(Object)</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html">ChangeableEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListener.html"><B>ChangeableListener</B></A> - interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A>.<DD>ChangeableListener.java
+
+
+ Created: Wed Jul 19 17:28:19 2000<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>ChangeableListenerSupport</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A>.<DD>ChangeableListenerSupport.java
+
+
+ Created: Thu Jul 20 17:58:39 2000<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html#ChangeableListenerSupport()"><B>ChangeableListenerSupport()</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html"><B>ChangeListenerSupport</B></A> - class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html">ChangeListenerSupport</A>.<DD>ChangeListenerSupport.java
+
+
+ Created: Tue Apr 4 13:31:52 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#ChangeListenerSupport()"><B>ChangeListenerSupport()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html">ChangeListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>
+<DD>method signalled after a change has occured to a multiple alignment
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>changeOccurred(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListener.html#changeOccurred(uk.ac.man.bioinf.util.ChangeableEvent)"><B>changeOccurred(ChangeableEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>
+<DD>Method called when a change occurs
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>changeOccurred(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#characters(char[], int, int)"><B>characters(char[], int, int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#characters(java.lang.String)"><B>characters(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html#charArray"><B>charArray</B></A> -
+Variable in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html">DefaultFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#charAt(int)"><B>charAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html">SequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#charAt(int)"><B>charAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#check(java.io.File)"><B>check(File)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><B>checkComplexSequenceType(ComplexElement)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement[])"><B>checkComplexSequenceType(ComplexElement[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRange(int)"><B>checkGappedRange(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRangeForInsert(int)"><B>checkGappedRangeForInsert(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>CheckMotifLocationAgainstPrints</B></A> - class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>.<DD>CheckMotifLocationAgainstPrints.java
+
+ This class moves through all the SequenceAlignments in the current
+ directory.<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#CheckMotifLocationAgainstPrints()"><B>CheckMotifLocationAgainstPrints()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)"><B>checkRange(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#checkSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>checkSequence(String, String, GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)"><B>checkSequenceType(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)"><B>checkSequenceType(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])"><B>checkSequenceType(Element[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>Check if all these elements are of a valid type
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])"><B>checkSequenceType(Element[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#chompLeadingGaps(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>chompLeadingGaps(GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>This removes all of the leading gaps from a gapped sequence, and
+ then returns the number of gaps removed.
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#chompTrailingGaps(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>chompTrailingGaps(GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>Removes and returns the number of trailing gaps off a gapped
+ sequence.
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html"><B>ChunkyListModel</B></A> - class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>.<DD>ChunkyListModel.java
+
+ This is a small extension to the list model class.<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#ChunkyListModel()"><B>ChunkyListModel()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html"><B>Cinema</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html">Cinema</A>.<DD>Cinema.java
+
+
+ Created: Fri May 26 22:04:20 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html#CINEMA_BOOT"><B>CINEMA_BOOT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html#CINEMA_COLOR_FACTORY"><B>CINEMA_COLOR_FACTORY</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html#CINEMA_COLOR_SELECTOR"><B>CINEMA_COLOR_SELECTOR</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html#CINEMA_CONSENSUS"><B>CINEMA_CONSENSUS</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html#CINEMA_CONSENSUS_DISPLAY"><B>CINEMA_CONSENSUS_DISPLAY</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html#CINEMA_CORE_GUI"><B>CINEMA_CORE_GUI</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html#CINEMA_CORE_VIEW"><B>CINEMA_CORE_VIEW</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html#CINEMA_DEBUG"><B>CINEMA_DEBUG</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_FILE_PERSIST"><B>CINEMA_FILE_PERSIST</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_GO"><B>CINEMA_GO</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html#CINEMA_GROUPS"><B>CINEMA_GROUPS</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html">CinemaGroupIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_INVOKER"><B>CINEMA_INVOKER</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_MENU_BUILDER"><B>CINEMA_MENU_BUILDER</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_MENU_SYSTEM"><B>CINEMA_MENU_SYSTEM</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html#CINEMA_MOTIF"><B>CINEMA_MOTIF</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html">CinemaMotifIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_MULTIPLE_CONSENSUS"><B>CINEMA_MULTIPLE_CONSENSUS</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_PERSIST"><B>CINEMA_PERSIST</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html#CINEMA_QUIT_EXIT"><B>CINEMA_QUIT_EXIT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_REGEXP"><B>CINEMA_REGEXP</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_RESIZE_ELEMENTS"><B>CINEMA_RESIZE_ELEMENTS</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_SEQUENCE_MENU"><B>CINEMA_SEQUENCE_MENU</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html#CINEMA_SHARED"><B>CINEMA_SHARED</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_SLAVE_VIEWER"><B>CINEMA_SLAVE_VIEWER</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html#CINEMA_SPLASH"><B>CINEMA_SPLASH</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_STATUS"><B>CINEMA_STATUS</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_SYSTEM_EVENTS"><B>CINEMA_SYSTEM_EVENTS</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html#Cinema()"><B>Cinema()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html">Cinema</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html"><B>CinemaActionProvider</B></A> - interface uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>.<DD>CinemaActionProvider.java
+
+
+ Created: Tue May 16 16:32:25 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html"><B>CinemaAlignmentFrame</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>.<DD>CinemaAlignmentFrame.java
+
+ This class provides a basic CinemaAlignmentFrame which consists of
+ a JScrollPane, with an JAlignmentViewer in the middle,
+ JAlignmentButton panel down the right hand side and a
+ JAlignmentRuler across the bottom.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#CinemaAlignmentFrame(java.lang.String, java.lang.String)"><B>CinemaAlignmentFrame(String, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#CinemaAlignmentFrame(java.lang.String, java.lang.String, boolean)"><B>CinemaAlignmentFrame(String, String, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#CinemaAlignmentFrame(java.lang.String, java.lang.String, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>CinemaAlignmentFrame(String, String, SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html"><B>CinemaAnchorManager</B></A> - class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>.<DD>CinemaAnchorManager.java
+
+ This group takes care of the anchoring groups, and adding and
+ removing appropriate listeners to the main alignment viewer, and
+ then adding and removing gaps.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#CinemaAnchorManager(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)"><B>CinemaAnchorManager(CinemaGroupModule)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>CinemaBoot</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>.<DD>CinemaBoot.java
+
+
+ Created: Mon May 29 17:58:12 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#CinemaBoot()"><B>CinemaBoot()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>CinemaBootIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A>.<DD>CinemaBootIdentifier.java
+
+
+ Created: Mon May 29 18:09:22 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>CinemaColorFactory</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>.<DD>CinemaColorFactory.java
+
+
+ Created: Fri Feb 9 11:49:21 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#CinemaColorFactory()"><B>CinemaColorFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>CinemaColorIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A>.<DD>CinemaColorIdentifier.java
+
+
+ Created: Sun May 28 22:34:00 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>CinemaColorSelector</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>.<DD>CinemaColorSelector.java
+
+ Created: Sun May 28 22:14:13 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#CinemaColorSelector()"><B>CinemaColorSelector()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>CinemaCommandLineParser</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>.<DD>CinemaCommandLineParser.java
+
+ This module is responsible for parsing the command line to Cinema
+ and invoking what ever actions are necessary.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#CinemaCommandLineParser()"><B>CinemaCommandLineParser()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>CinemaCommandLineParserIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html">CinemaCommandLineParserIdentifier</A>.<DD>The identifier for the CinemaCommandLineParser module.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html"><B>CinemaConsensus</B></A> - class uk.ac.man.bioinf.apps.cinema.consens [...]
+Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html"><B>CinemaConsensusCalculatorMetaData</B></A> - interface uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A>.<DD>CinemaConsensusCalculatorMetaData.java
+
+
+ Created: Thu Jul 27 16:45:21 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>CinemaConsensusDisplay</B></A> - class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>.<DD>CinemaConsensusDisplay.java
+
+
+ Created: Thu Nov 9 15:06:00 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#CinemaConsensusDisplay()"><B>CinemaConsensusDisplay()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html"><B>CinemaConsensusIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A>.<DD>CinemaConsensusIdentifier.java
+
+
+ Created: Mon Jul 24 18:55:00 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>CinemaCoreGui</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>.<DD>CinemaCoreGui.java
+
+ This module defines the core Gui for cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#CinemaCoreGui()"><B>CinemaCoreGui()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html"><B>CinemaCoreIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A>.<DD>CinemaCoreIdentifier.java
+
+
+ Created: Sun May 7 18:16:43 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>CinemaCoreView</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>.<DD>CinemaCoreView.java
+
+ This class provides an easy interface to many of the display
+ functions of Cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#CinemaCoreView()"><B>CinemaCoreView()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>CinemaDebug</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>.<DD>CinemaDebug.java
+
+ This class provides the Debugging architecture implementation for
+ Cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html"><B>CinemaDebug</B></A> - class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>.<DD>CinemaDebug.java
+
+ This class provides the Debugging architecture implementation for
+ Cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>CinemaDebug.DebugImpl</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>CinemaDebug.DebugImpl</B></A> - class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.htm [...]
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html#CinemaDebug.DebugImpl()"><B>CinemaDebug.DebugImpl()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#CinemaDebug()"><B>CinemaDebug()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#CinemaDebug()"><B>CinemaDebug()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>CinemaFileOptionableExceptionHandler</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>.<DD>CinemaFileOptionableExceptionHandler.java
+
+
+ Created: Mon May 14 16:21:58 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#CinemaFileOptionableExceptionHandler()"><B>CinemaFileOptionableExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>CinemaFilePersist</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A>.<DD>CinemaFilePersist.java
+
+
+ Created: Tue Jan 30 15:53:21 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#CinemaFilePersist()"><B>CinemaFilePersist()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html"><B>CinemaFramedActionProvider</B></A> - interface uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>.<DD>CinemaFramedActionProvider.java
+
+
+ Created: Fri Oct 13 17:04:25 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>CinemaGo</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html">CinemaGo</A>.<DD>CinemaGo.java
+
+ This class actually makes the Cinema gui visible.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html#CinemaGo()"><B>CinemaGo()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html">CinemaGo</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>CinemaGroup</B></A> - class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>.<DD>CinemaGroup.java
+
+ This class is more or less entirely a wrapper around the
+ HashMap, and just switches all of the return types back to
+ something sane.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#CinemaGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.lang.String)"><B>CinemaGroup(CinemaGroupManager, SequenceAlignment, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>CinemaGroupFrame</B></A> - class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>.<DD>CinemaGroupFrame.java
+
+
+ Created: Fri Jun 2 19:19:00 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#CinemaGroupFrame(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)"><B>CinemaGroupFrame(CinemaGroupModule)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html"><B>CinemaGroupIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html">CinemaGroupIdentifier</A>.<DD>CinemaGroupIdentifier.java
+
+
+ Created: Thu May 25 18:53:58 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>CinemaGroupManager</B></A> - class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>.<DD>CinemaGroupManager.java
+
+
+ Created: Mon May 22 17:36:04 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#CinemaGroupManager(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)"><B>CinemaGroupManager(CinemaGroupModule)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html"><B>CinemaGroupModule</B></A> - class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>.<DD>CinemaGroupModule.java
+
+
+ Created: Tue May 23 15:42:48 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#CinemaGroupModule()"><B>CinemaGroupModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>.<DD>CinemaGuiModule.java
+
+
+ Created: Fri May 26 21:04:15 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#CinemaGuiModule()"><B>CinemaGuiModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>CinemaInvoker</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>.<DD>CinemaInvoker.java
+
+
+ Created: Tue Apr 25 20:24:30 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#CinemaInvoker()"><B>CinemaInvoker()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>CinemaMenuBuilder</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html">CinemaMenuBuilder</A>.<DD>CinemaMenuBuilder.java
+
+ This class builds a menu system based upon the module configuration
+ information.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html#CinemaMenuBuilder()"><B>CinemaMenuBuilder()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html">CinemaMenuBuilder</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>CinemaMenuSystem</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html">CinemaMenuSystem</A>.<DD>CinemaMenuSystem.java
+
+
+ Created: Tue May 16 14:24:27 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#CinemaMenuSystem()"><B>CinemaMenuSystem()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html">CinemaMenuSystem</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>.<DD>CinemaModule.java
+
+ Most modules for Cinema should extend this interface.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#CinemaModule()"><B>CinemaModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html"><B>CinemaModuleCoreIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A>.<DD>CinemaModuleCoreIdentifer.java
+
+
+ Created: Fri May 26 21:39:17 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>CinemaModuleFactoryInstance</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html">CinemaModuleFactoryInstance</A>.<DD>CinemaModuleFactoryInstance.java
+
+ This class adds some reporting functions to the superclass.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html#CinemaModuleFactoryInstance()"><B>CinemaModuleFactoryInstance()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html">CinemaModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html"><B>CinemaMotifFrame</B></A> - class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>.<DD>CinemaMotifFrame.java
+
+
+ Created: Tue Jan 16 13:54:41 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#CinemaMotifFrame(uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel, uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule)"><B>CinemaMotifFrame(NamedAlignmentSelectionModel, CinemaMotifModule)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html"><B>CinemaMotifIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html">CinemaMotifIdentifier</A>.<DD>CinemaMotifIdentifier.java
+
+
+ Created: Mon Jan 15 15:16:05 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>CinemaMotifModule</B></A> - class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A>.<DD>CinemaMotifModule.java
+
+ This module is designed to handle motif selection and viewing
+ within Cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#CinemaMotifModule()"><B>CinemaMotifModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>CinemaMultipleConsensusViewer</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>.<DD>CinemaMultipleConsensusViewer.java
+
+
+ Created: Fri Jun 23 12:09:24 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#CinemaMultipleConsensusViewer()"><B>CinemaMultipleConsensusViewer()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>CinemaPersist</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A>.<DD>CinemaPersist.java
+
+ Provides the OptionHandler which classes need to implement persistance.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#CinemaPersist()"><B>CinemaPersist()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>CinemaProperties</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html">CinemaProperties</A>.<DD>CinemaProperties.java
+
+ This are all of the property names that the CinemaModule signals
+ changes for.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>CinemaRegexp</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html">CinemaRegexp</A>.<DD>CinemaRegexp.java
+
+ Provides support for various regexp searching facilities.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html#CinemaRegexp()"><B>CinemaRegexp()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html">CinemaRegexp</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>CinemaResizeElements</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html">CinemaResizeElements</A>.<DD>CinemaResizeElements.java
+
+
+ Created: Wed Jul 26 14:40:14 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#CinemaResizeElements()"><B>CinemaResizeElements()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html">CinemaResizeElements</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html"><B>CinemaResources</B></A> - class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>.<DD>CinemaResources.java
+
+ The purpose of this class is to provide access to the resources
+ that cinema needs in a manner which is appropriate and simple both
+ during development time and after deployment.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#CinemaResources()"><B>CinemaResources()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>CinemaSequenceMenu</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>.<DD>CinemaSequenceMenu.java
+
+
+ Created: Mon May 22 14:04:57 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#CinemaSequenceMenu()"><B>CinemaSequenceMenu()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>CinemaShared</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html">CinemaShared</A>.<DD>CinemaShared.java
+
+
+ Created: Tue Sep 12 17:22:26 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html#CinemaShared()"><B>CinemaShared()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html">CinemaShared</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html"><B>CinemaSharedIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A>.<DD>CinemaSharedIdentifier.java
+
+
+ Created: Fri Sep 15 13:45:25 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>CinemaSharedQuitExit</B></A> - class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html">CinemaSharedQuitExit</A>.<DD>CinemaSharedQuitExit.java
+
+
+ Created: Fri Sep 15 13:51:24 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html#CinemaSharedQuitExit()"><B>CinemaSharedQuitExit()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html">CinemaSharedQuitExit</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>CinemaSlaveViewerModule</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html">CinemaSlaveViewerModule</A>.<DD>CinemaSlaveViewerModule.java
+
+ Generates arbitrary numbers of Slave Viewers.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html#CinemaSlaveViewerModule()"><B>CinemaSlaveViewerModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html">CinemaSlaveViewerModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html"><B>CinemaSplash</B></A> - class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html">CinemaSplash</A>.<DD>CinemaSplash.java
+
+
+ Created: Tue Dec 12 17:42:27 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#CinemaSplash()"><B>CinemaSplash()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html">CinemaSplash</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html"><B>CinemaStatusInformation</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html">CinemaStatusInformation</A>.<DD>CinemaStatusInformation.java
+
+ A utility class which provides what are hopefully useful status bar
+ information messages about what Cinema is currently showing.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#CinemaStatusInformation()"><B>CinemaStatusInformation()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html">CinemaStatusInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>CinemaSystemEvents</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>.<DD>CinemaSystemEvents.java
+
+
+ Created: Thu Apr 20 18:26:56 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#CinemaSystemEvents()"><B>CinemaSystemEvents()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html"><B>CinemaTestLaunch</B></A> - class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html">CinemaTestLaunch</A>.<DD>CinemaTestLaunch.java
+
+
+ Created: Wed Apr 19 18:29:17 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#CinemaTestLaunch()"><B>CinemaTestLaunch()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html">CinemaTestLaunch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html"><B>CinemaTestModuleLaunch</B></A> - class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html">CinemaTestModuleLaunch</A>.<DD>CinemaTestModuleLaunch.java
+
+
+ Created: Wed May 24 18:37:22 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html#CinemaTestModuleLaunch()"><B>CinemaTestModuleLaunch()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html">CinemaTestModuleLaunch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html"><B>CinemaUtilityIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A>.<DD>CinemaUtilityIdentifier.java
+
+
+ Created: Thu May 25 14:27:34 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html"><B>CinemaXMLParserFactory</B></A> - class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html">CinemaXMLParserFactory</A>.<DD>CinemaXMLParserFactory.java
+
+
+ Created: Mon Sep 18 18:59:17 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html#CinemaXMLParserFactory()"><B>CinemaXMLParserFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html">CinemaXMLParserFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#classEnd()"><B>classEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#clear()"><B>clear()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#clear()"><B>clear()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Clear the list.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#clear()"><B>clear()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Clear the list.
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#clear()"><B>clear()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#clearAllSelections()"><B>clearAllSelections()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#clearAllSequenceColors()"><B>clearAllSequenceColors()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#clearExceptions()"><B>clearExceptions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A>
+<DD>Clears all exceptions that have been stored.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#clearExceptions()"><B>clearExceptions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A>
+<DD>Clears all exceptions that have been stored.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#clearGroups()"><B>clearGroups()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#clearSelection()"><B>clearSelection()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#clearSelection()"><B>clearSelection()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#clearSelection()"><B>clearSelection()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#clearSelection()"><B>clearSelection()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#clearSelection()"><B>clearSelection()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Clear all the selections in this model
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#clearSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>clearSelection(SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#clearSelection(java.lang.String)"><B>clearSelection(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#clearSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>clearSequenceColor(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#clearSequences()"><B>clearSequences()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Empty the group of sequences
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#clearSequences()"><B>clearSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#clearSequences()"><B>clearSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>clearSequenceTitleColor(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>clearSequenceTitleColor(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#clone()"><B>clone()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#close()"><B>close()</B></A> -
+Method in interface uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#close()"><B>close()</B></A> -
+Method in class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html"><B>CollectionPrinter</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html">CollectionPrinter</A>.<DD>CollectionPrinter.java
+
+
+ Created: Thu Jul 20 19:47:52 2000<DT><A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html#CollectionPrinter()"><B>CollectionPrinter()</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html">CollectionPrinter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>ColorFastAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html">ColorFastAlignmentViewerCellRenderer</A>.<DD>ColorFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html#ColorFastAlignmentViewerCellRenderer()"><B>ColorFastAlignmentViewerCellRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html">ColorFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html"><B>ColorGenerator</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A>.<DD>ColorGenerator.java
+
+ This class generates a stream of colours, cycling through all of
+ the colours in the list until it has finished.<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html#ColorGenerator()"><B>ColorGenerator()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html#ColorGenerator(java.awt.Color[])"><B>ColorGenerator(Color[])</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html"><B>ColorList</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>.<DD>ColorList.java
+
+ This class is similar to ColorGenerator, except that instead of
+ cycling through the colours it presents them as a list
+
+ Created: Thu Jun 8 17:37:23 2000<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#ColorList()"><B>ColorList()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#ColorList(java.awt.Color[])"><B>ColorList(Color[])</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html"><B>ColorMap</B></A> - interface uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>.<DD>ColorMap.java
+
+ The interface to support color mapping of elements in a sequence
+ alignment.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>ColormapColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#ColormapColorMapMetaData()"><B>ColormapColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html"><B>ColorMapException</B></A> - exception uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html">ColorMapException</A>.<DD>ColorMapException.java
+
+
+ Created: Mon Apr 10 09:06:32 2000<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html#ColorMapException(java.lang.String)"><B>ColorMapException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html">ColorMapException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html"><B>ColorMapMetaData</B></A> - interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>.<DD>ColorMapMetaData.java
+
+ Many of the colour maps available need to be treated in different
+ ways.<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#colors"><B>colors</B></A> -
+Variable in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorStore.html"><B>ColorStore</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorStore.html">ColorStore</A>.<DD>ColorStore.java
+
+ This is a static place holder of various lists of colours.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html#COMMAND_LINE_PARSER"><B>COMMAND_LINE_PARSER</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html">CinemaCommandLineParserIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#compareTo(java.lang.Object)"><B>compareTo(Object)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Compares another rectangle to this one.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#compareTo(java.lang.Object)"><B>compareTo(Object)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Compares this point to another.
+<DT><A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>.<DD>ComplexEditableGappedSequence.java
+
+
+ Created: Wed Dec 6 20:08:32 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html"><B>ComplexElement</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>.<DD>ComplexElement.java
+
+
+ Created: Mon Feb 28 20:41:07 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html"><B>ComplexElementAndModificationTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html">ComplexElementAndModificationTest</A>.<DD>ComplexElementAndModificationTest.java
+
+
+ Created: Tue Feb 29 11:32:15 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html#ComplexElementAndModificationTest()"><B>ComplexElementAndModificationTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html">ComplexElementAndModificationTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>ComplexElementFactory</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>.<DD>ComplexElementFactory.java
+
+
+ Created: Tue Feb 29 00:21:47 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#ComplexElementFactory()"><B>ComplexElementFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>ComplexElementFactoryInterface</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A>.<DD>ComplexElementFactoryInterface.java
+
+
+ Created: Wed Mar 1 12:40:54 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>ComplexSequence</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>.<DD>ComplexSequence.java
+
+
+ Created: Wed Nov 22 17:56:08 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html"><B>ComplexSequenceTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html">ComplexSequenceTest</A>.<DD>ComplexSequenceTest.java
+
+
+ Created: Mon Nov 27 14:09:29 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html#ComplexSequenceTest()"><B>ComplexSequenceTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html">ComplexSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>ComplexSequenceType</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>.<DD>ComplexSequenceType.java
+
+
+ Created: Tue Feb 29 11:25:27 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html"><B>ConfigNode</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>.<DD>ConfigNode.java
+
+
+ Created: Tue May 9 21:45:13 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#ConfigNode()"><B>ConfigNode()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#configStart(org.xml.sax.Attributes)"><B>configStart(Attributes)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html"><B>ConsensusCalculator</B></A> - interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A>.<DD>ConsensusCalculator.java
+
+
+ Created: Thu Jun 15 15:11:33 2000<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html"><B>ConsensusIdentifier</B></A> - class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html">ConsensusIdentifier</A>.<DD>ConsensusIdentifier.java
+
+
+ Created: Mon Oct 16 15:40:30 2000<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html#ConsensusIdentifier(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>ConsensusIdentifier(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html">ConsensusIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html#ConsensusIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>ConsensusIdentifier(Source, SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html">ConsensusIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html"><B>ConsensusPercentageIDColorMap</B></A> - class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>.<DD>ConsensusPercentageIDColorMap.java
+
+
+ Created: Fri Jun 23 17:57:45 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#ConsensusPercentageIDColorMap(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>ConsensusPercentageIDColorMap(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>ConsensusSequence</B></A> - interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>.<DD>ConsensusSequence.java
+
+
+ Created: Thu Jun 15 15:32:13 2000<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#contains(int)"><B>contains(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#contains(int, int)"><B>contains(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Determines whether a point is contained in this region.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#contains(uk.ac.man.bioinf.module.Module)"><B>contains(Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Returns whether a module is contained in this list.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#contains(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>contains(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Returns whether a module identifier is contained in this list.
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#contains(java.lang.Object)"><B>contains(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#contains(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>contains(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Determines whether a point is contained in this region.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)"><B>containsSequence(Sequence)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Does this group contain the sequence
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)"><B>containsSequence(Sequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)"><B>containsSequence(Sequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#convertYToRow(int)"><B>convertYToRow(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html">SwappingListBasicUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#copyInto(java.lang.Object[])"><B>copyInto(Object[])</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#createColorMapInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>createColorMapInstance(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html">InstancePerAlignmentColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#createDefaultModel()"><B>createDefaultModel()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">WholeNumberField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html#createDefaultModel()"><B>createDefaultModel()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#createException(int, char)"><B>createException(int, char)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html#createModification(java.lang.String, char)"><B>createModification(String, char)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html">ModificationFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#createMouseInputListener()"><B>createMouseInputListener()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html">SwappingListBasicUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#createNewGroup()"><B>createNewGroup()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#createNewGroup(java.lang.String)"><B>createNewGroup(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#createNewGroup(java.lang.String, java.awt.Color)"><B>createNewGroup(String, Color)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html#createRNAResidues()"><B>createRNAResidues()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html">ComplexSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#createUI(javax.swing.JComponent)"><B>createUI(JComponent)</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#createUI(javax.swing.JComponent)"><B>createUI(JComponent)</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>CursorLessFastAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html">CursorLessFastAlignmentViewerCellRenderer</A>.<DD>CursorLessFastAlignmentViewerCellRenderer.java
+
+
+ Created: Thu Jul 13 17:59:36 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html#CursorLessFastAlignmentViewerCellRenderer(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>CursorLessFastAlignmentViewerCellRenderer(JAlignmentViewer)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html">CursorLessFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#CYSTEINE"><B>CYSTEINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html#CYTOSINE"><B>CYTOSINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html#CYTOSINE"><B>CYTOSINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_D_"><!-- --></A><H2>
+<B>D</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>DatabaseIdentifier</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A>.<DD>DatabaseIdentifier.java
+
+
+ Created: Wed Jul 5 14:11:46 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#DatabaseIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, java.lang.String)"><B>DatabaseIdentifier(Source, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#debug"><B>debug</B></A> -
+Static variable in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>This is the main switch variable.
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html"><B>Debug</B></A> - class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>.<DD>Debug.java
+
+ This forms the basis of the Debugging architecture.<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#Debug()"><B>Debug()</B></A> -
+Constructor for class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html"><B>DebugInterface</B></A> - interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>.<DD>DebugInterface.java
+
+
+ Created: Wed Mar 1 22:15:41 2000<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>DebugMultiplexer</B></A> - class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>.<DD>DebugMultiplexer.java
+
+ This class can be used to multiplex other DebugInterface
+ interfaces.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#debugScreenDump()"><B>debugScreenDump()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html"><B>DecimalField</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">DecimalField</A>.<DD>Provides a validated field that only accepts decimal numbers.<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html#DecimalField(double, int, java.text.NumberFormat)"><B>DecimalField(double, int, NumberFormat)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">DecimalField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html#DecimalField(int, java.text.NumberFormat)"><B>DecimalField(int, NumberFormat)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">DecimalField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>DefaultAlignmentSelectionRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html">DefaultAlignmentSelectionRenderer</A>.<DD>DefaultAlignmentSelectionRenderer.java
+
+
+ Created: Wed Mar 7 18:59:56 2001<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html#DefaultAlignmentSelectionRenderer()"><B>DefaultAlignmentSelectionRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html">DefaultAlignmentSelectionRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>DefaultAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html">DefaultAlignmentViewerCellRenderer</A>.<DD>DefaultAlignmentViewerCellRenderer.java
+
+
+ Created: Mon Mar 20 20:23:12 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html#DefaultAlignmentViewerCellRenderer()"><B>DefaultAlignmentViewerCellRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html">DefaultAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>DefaultColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#DefaultColorMapMetaData()"><B>DefaultColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>DefaultComplexElement</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>.<DD>DefaultComplexElement.java
+
+
+ Created: Mon Feb 28 20:42:48 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>DefaultComplexSequence</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>.<DD>DefaultComplexSequence.java
+
+
+ Created: Fri Nov 24 14:08:23 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#DefaultComplexSequence(uk.ac.man.bioinf.sequence.complex.ComplexElement[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultComplexSequence(ComplexElement[], ComplexSequenceType, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#DefaultComplexSequence(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultComplexSequence(Residue[], ComplexSequenceType, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>DefaultComplexSequenceType</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>.<DD>DefaultComplexSequenceType.java
+
+
+ Created: Mon Nov 27 16:05:27 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#DefaultComplexSequenceType(uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.complex.Modification[], java.lang.String)"><B>DefaultComplexSequenceType(SequenceType, Modification[], String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>DefaultConsensusSequence</B></A> - class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>.<DD>DefaultConsensusSequence.java
+
+
+ Created: Thu Jun 15 17:00:04 2000<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#DefaultConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>DefaultConsensusSequence(ConsensusCalculator)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html"><B>DefaultDebug</B></A> - class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html">DefaultDebug</A>.<DD>DefaultDebug.java
+
+ Simple Debug interface which prints things to screen
+
+ Created: Thu Mar 9 17:57:34 2000<DT><A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html#DefaultDebug()"><B>DefaultDebug()</B></A> -
+Constructor for class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html">DefaultDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>DefaultEditableSequence</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>.<DD>DefaultEditableSequence.java
+
+
+ Created: Thu Mar 2 20:27:46 2000<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#DefaultEditableSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultEditableSequence(Element[], SequenceType, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#DefaultEditableSequence(uk.ac.man.bioinf.sequence.Sequence)"><B>DefaultEditableSequence(Sequence)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#DefaultEditableSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultEditableSequence(Sequence, SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>DefaultFastAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html">DefaultFastAlignmentViewerCellRenderer</A>.<DD>DefaultFastAlignmentViewerCellRenderer.java
+
+
+ Created: Mon Apr 17 20:11:46 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html#DefaultFastAlignmentViewerCellRenderer()"><B>DefaultFastAlignmentViewerCellRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html">DefaultFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html"><B>DefaultFileDebug</B></A> - class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html">DefaultFileDebug</A>.<DD>DefaultFileDebug.java
+
+
+ Created: Sun May 7 23:46:57 2000<DT><A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html#DefaultFileDebug(java.io.File)"><B>DefaultFileDebug(File)</B></A> -
+Constructor for class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html">DefaultFileDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>DefaultGappedComplexSequence</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>.<DD>DefaultGappedComplexSequence.java
+
+
+ Created: Tue Dec 5 16:55:11 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#DefaultGappedComplexSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)"><B>DefaultGappedComplexSequence(Element[], ComplexSequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>DefaultGappedSequence</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>.<DD>DefaultGappedSequence.java
+
+
+ Created: Sat Mar 4 12:28:57 2000<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultGappedSequence(Element[], SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultGappedSequence(Element[], SequenceType, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>A new gapped sequence, with no gaps in it!
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.util.IntArrayList, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultGappedSequence(Element[], SequenceType, IntArrayList, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.util.IntArrayList)"><B>DefaultGappedSequence(Sequence, IntArrayList)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>DefaultGappedSequenceGroup</B></A> - class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>.<DD>DefaultGappedSequenceGroup.java
+
+
+ Created: Thu Jun 1 18:33:14 2000<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#DefaultGappedSequenceGroup()"><B>DefaultGappedSequenceGroup()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#defaultLocale"><B>defaultLocale</B></A> -
+Variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>DefaultModuleContext</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html">DefaultModuleContext</A>.<DD>DefaultModuleContext.java
+
+
+ Created: Tue May 23 15:03:25 2000<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html#DefaultModuleContext(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleStorageStructure)"><B>DefaultModuleContext(ModuleIdentifier, ModuleStorageStructure)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html">DefaultModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>DefaultModuleFactoryInstance</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>.<DD>DefaultModuleFactoryInstance.java
+
+
+ Created: Thu May 11 13:02:22 2000<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#DefaultModuleFactoryInstance()"><B>DefaultModuleFactoryInstance()</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#defaultPack()"><B>defaultPack()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Pack the frame if the size hasnt been sized by its options
+<DT><A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html"><B>DefaultParserExceptionHandler</B></A> - class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html">DefaultParserExceptionHandler</A>.<DD>This parser exception handler does very little.<DT><A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html#DefaultParserExceptionHandler()"><B>DefaultParserExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html">DefaultParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>DefaultSequence</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>.<DD>DefaultSequence.java
+
+
+ Created: Thu Mar 2 15:32:25 2000<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultSequence(Element[], SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultSequence(Element[], SequenceType, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Sequence)"><B>DefaultSequence(Sequence)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultSequence(Sequence, SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>DefaultSequenceAlignment</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>.<DD>DefaultSequenceAlignment.java
+
+ A class to model the multiple sequence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.Element[][], uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultSequenceAlignment(Element[][], SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultSequenceAlignment(GappedSequence[], SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[])"><B>DefaultSequenceAlignment(GappedSequence[], SequenceType, int[])</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[], uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultSequenceAlignment(GappedSequence[], SequenceType, int[], Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultSequenceAlignment(SequenceAlignment, SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.SequenceType)"><B>DefaultSequenceAlignment(SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>DefaultSequenceAlignment(SequenceType, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>DefaultSequenceCursor</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>.<DD>DefaultSequenceCursor.java
+
+
+ Created: Tue Apr 4 12:49:30 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#DefaultSequenceCursor()"><B>DefaultSequenceCursor()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>DefaultXMLParser</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html">DefaultXMLParser</A>.<DD>DefaultXMLParser.java
+
+
+ Created: Mon May 8 21:08:32 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html#DefaultXMLParser()"><B>DefaultXMLParser()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html">DefaultXMLParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#DELETE"><B>DELETE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>
+<DD>Event type indicated a sequence has been removed from the
+ sequence alignment
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html#DELETE"><B>DELETE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int)"><B>deleteElementAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>
+<DD>Delete the element at index.
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAt(int)"><B>deleteElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int, int)"><B>deleteElementAt(int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>
+<DD>Delete the elements starting at index for the specified length
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAt(int, int)"><B>deleteElementAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#deleteElementAtQuietly(int)"><B>deleteElementAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAtQuietly(int)"><B>deleteElementAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>Do the actual deletion but dont do any event signalling.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)"><B>deleteGapAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>Delete the element at index.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#deleteGapAt(int)"><B>deleteGapAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int)"><B>deleteGapAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#deleteGapAt(int)"><B>deleteGapAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)"><B>deleteGapAt(int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>Delete the elements starting at index for the specified length
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#deleteGapAt(int, int)"><B>deleteGapAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int, int)"><B>deleteGapAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#deleteGapAt(int, int)"><B>deleteGapAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#deleteGapAtQuietly(int)"><B>deleteGapAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#deleteGapAtQuietly(int)"><B>deleteGapAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAtQuietly(int)"><B>deleteGapAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#deleteGapsAt(int, int, int)"><B>deleteGapsAt(int, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#deleteGapsAt(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int)"><B>deleteGapsAt(SequenceAlignmentPoint, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#deleteGapsAtCursor(int)"><B>deleteGapsAtCursor(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#destroy()"><B>destroy()</B></A> -
+Method in interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>Gracefully close down the thread
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#destroy()"><B>destroy()</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#destroy()"><B>destroy()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/Direction.html"><B>Direction</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Direction.html">Direction</A>.<DD>Direction.java
+
+ EnumeratedType defining directions.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#dispose()"><B>dispose()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#dispose()"><B>dispose()</B></A> -
+Method in interface uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#dispose()"><B>dispose()</B></A> -
+Method in class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>DNANucleotide</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>.<DD>DNANucleotide.java
+
+
+ Created: Sun Sep 24 17:44:04 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNAResidue.html"><B>DNAResidue</B></A> - interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>.<DD>DNAResidue.java
+
+ An interface to represent a DNA residue.<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>DNASequenceType</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A>.<DD>DNASequenceType.java
+
+ This class represents the DNA sequence type, allowing only a set
+ of particular bases.<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#doRun()"><B>doRun()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html"><B>DoubleArrayColorMap</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html">DoubleArrayColorMap</A>.<DD>DoubleArrayColorMap.java
+
+ This class takes a series of doubles, a list of colours and a
+ sequence alignment and turns them into a colour map.<DT><A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html#DoubleArrayColorMap(double[][], uk.ac.man.bioinf.gui.color.ColorList)"><B>DoubleArrayColorMap(double[][], ColorList)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html">DoubleArrayColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#DOWN"><B>DOWN</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_E_"><!-- --></A><H2>
+<B>E</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/util/Direction.html#EAST"><B>EAST</B></A> -
+Static variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Direction.html">Direction</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html"><B>EditableSequence</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>.<DD>EditableSequence.java
+
+
+ Created: Wed Mar 1 19:39:40 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html"><B>EditableSequenceTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html">EditableSequenceTest</A>.<DD>EditableSequenceTest.java
+
+
+ Created: Fri Mar 3 16:08:35 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html#EditableSequenceTest()"><B>EditableSequenceTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html">EditableSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#eh"><B>eh</B></A> -
+Variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#eh"><B>eh</B></A> -
+Variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Element.html"><B>Element</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Element.html">Element</A>.<DD>Element.java
+
+ This interface defines an element within a sequence.<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#elementAt(int)"><B>elementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements"><B>elements</B></A> -
+Variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#elements()"><B>elements()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>EmptyGappedSequence</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>.<DD>EmptyGappedSequence.java
+
+
+ Created: Tue Nov 7 18:15:06 2000<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html"><B>EmptySequence</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>.<DD>EmptySequence.java
+
+
+ Created: Mon Feb 5 17:53:37 2001<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>EmptySequenceAlignment</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>.<DD>EmptySequenceAlignment.java
+
+
+ Created: Wed Apr 19 17:23:30 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>EmptySequenceType</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>.<DD>EmptySequenceType.java
+
+
+ Created: Tue Aug 1 17:22:00 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#endDocument()"><B>endDocument()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#endElement(java.lang.String, java.lang.String, java.lang.String)"><B>endElement(String, String, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#endPrefixMapping(java.lang.String)"><B>endPrefixMapping(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#enqueue(uk.ac.man.bioinf.apps.invoker.AnonInvoker)"><B>enqueue(AnonInvoker)</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#ensureCapacity(int)"><B>ensureCapacity(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#ensureCapacity(int)"><B>ensureCapacity(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#ensureSequencePointIsVisible(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>ensureSequencePointIsVisible(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#enumerationEnd()"><B>enumerationEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#EQUALS"><B>EQUALS</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#equals(uk.ac.man.bioinf.util.IntArrayList)"><B>equals(IntArrayList)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Compares two SARectangles for equality (ie: whether they have the
+ same dimension and location).
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Ascertains the equality of a given point to this
+ object.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Ascertains the equality of a given dimension to this
+ object.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#error(org.xml.sax.SAXParseException)"><B>error(SAXParseException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html"><B>ExceptionHandler</B></A> - interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html">ExceptionHandler</A>.<DD>ExceptionHandler.java
+
+ This class handles exceptions!
+
+ Created: Fri May 14 14:12:58 1999<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html"><B>ExpasySequenceRetriever</B></A> - class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>.<DD>ExpasySequenceRetriever.java
+
+ Retrieves Swissprot sequence from Expasy.<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#ExpasySequenceRetriever()"><B>ExpasySequenceRetriever()</B></A> -
+Constructor for class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#ExpasySequenceRetriever(java.lang.String)"><B>ExpasySequenceRetriever(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>extendSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>extendSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>extendSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>extendSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>extendSelection(SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Start a selection at the given point
+</DL>
+<HR>
+<A NAME="_F_"><!-- --></A><H2>
+<B>F</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html"><B>FastAlignmentViewerCellRenderer</B></A> - interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>.<DD>FastAlignmentViewerCellRenderer.java
+
+ Although the JAlignmentViewer provides a pluggable renderer
+ architecture with the AlignmentViewerCellRenderer it has been found
+ that this has a fairly disasterous effect on performance of the
+ viewer particularly with respect to scrolling, due to the large
+ number of method calls and events to render a cell.<DT><A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>FastaSequenceParser</B></A> - class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html">FastaSequenceParser</A>.<DD>FastaSequenceParser.java
+
+
+ Created: Wed Feb 7 15:07:45 2001<DT><A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#FastaSequenceParser()"><B>FastaSequenceParser()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html">FastaSequenceParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#fatalError(org.xml.sax.SAXParseException)"><B>fatalError(SAXParseException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#fetchCinemaDirectoryString()"><B>fetchCinemaDirectoryString()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html#fetchMainBootName()"><B>fetchMainBootName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html">CinemaShared</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#fetchMainBootName()"><B>fetchMainBootName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#fetchMainBootName()"><B>fetchMainBootName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#fetchModuleSystemIdentifier()"><B>fetchModuleSystemIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#fetchModuleSystemIdentifier()"><B>fetchModuleSystemIdentifier()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#fetchModuleSystemIdentifier()"><B>fetchModuleSystemIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html"><B>FetchSequenceBySwissProtID</B></A> - class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html">FetchSequenceBySwissProtID</A>.<DD>FetchSequenceBySwissProtID.java
+
+ This class fetchs a
+ Created: Wed Feb 7 14:58:40 2001<DT><A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html#FetchSequenceBySwissProtID()"><B>FetchSequenceBySwissProtID()</B></A> -
+Constructor for class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html">FetchSequenceBySwissProtID</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html#FILE_INPUT"><B>FILE_INPUT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html#FILE_OUTPUT"><B>FILE_OUTPUT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html"><B>FileSaveableOptions</B></A> - class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html">FileSaveableOptions</A>.<DD>FileSaveableOptions.java
+
+ Provides Saveable Option support with files.<DT><A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html#FileSaveableOptions(java.io.File, uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)"><B>FileSaveableOptions(File, SystemEventProducer, OptionableExceptionHandler)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html">FileSaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>FileSequenceInput</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A>.<DD>FileSequenceInput is a that module covers sequence input into
+ Cinema via files.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#FileSequenceInput()"><B>FileSequenceInput()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>FileSequenceInputParserExceptionHandler</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html">FileSequenceInputParserExceptionHandler</A>.<DD>FileSequenceInputParserExceptionHandler handles parser exceptions
+ to do with parsing files, and will display a dialog box.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html#FileSequenceInputParserExceptionHandler()"><B>FileSequenceInputParserExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html">FileSequenceInputParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>FileSequenceOutput</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html">FileSequenceOutput</A>.<DD>FileSequenceOutput is a module that covers sequence output to a
+ file from Cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#FileSequenceOutput()"><B>FileSequenceOutput()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html">FileSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>FileSequenceParserExceptionHandler</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html">FileSequenceParserExceptionHandler</A>.<DD>FileSequenceParserExceptionHandler handles parser exceptions
+ to do with parsing files, and will display a dialog box.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html#FileSequenceParserExceptionHandler()"><B>FileSequenceParserExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html">FileSequenceParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>FileSource</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html">FileSource</A>.<DD>FileSource.java
+
+
+ Created: Fri Sep 8 18:57:27 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html#FileSource(java.io.File)"><B>FileSource(File)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html">FileSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#finalize()"><B>finalize()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#fireAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>fireAlignmentEvent(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#fireAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><B>fireAlignmentEvent(AlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>This function fires the MSA event to all the interested listeners, and also
+ signals the vetoable listeners, which are stored separately.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#fireAlignmentSelectionEvent(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><B>fireAlignmentSelectionEvent(AlignmentSelectionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html">AlignmentSelectionListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#fireChangeEvent()"><B>fireChangeEvent()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html#fireChangeEvent(uk.ac.man.bioinf.util.ChangeableEvent)"><B>fireChangeEvent(ChangeableEvent)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#fireChangeEvent(javax.swing.event.ChangeEvent)"><B>fireChangeEvent(ChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html">ChangeListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#fireCinemaPropertyChange(java.lang.String, java.lang.Object, java.lang.Object)"><B>fireCinemaPropertyChange(String, Object, Object)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#firePropertyChange(java.beans.PropertyChangeEvent)"><B>firePropertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#firePropertyChange(java.beans.PropertyChangeEvent)"><B>firePropertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#firePropertyChange(java.lang.String, int, int)"><B>firePropertyChange(String, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#firePropertyChange(java.lang.String, int, int)"><B>firePropertyChange(String, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)"><B>firePropertyChange(String, Object, Object)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)"><B>firePropertyChange(String, Object, Object)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>fireSequenceEvent(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#fireSequenceEvent(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>fireSequenceEvent(SequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>This function fires the sequence event to all the interested listeners.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#fireSystemEvent(uk.ac.man.bioinf.apps.systemevents.SystemEventOption)"><B>fireSystemEvent(SystemEventOption)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#fireSystemEvent(uk.ac.man.bioinf.apps.systemevents.SystemEventOption)"><B>fireSystemEvent(SystemEventOption)</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#fireSystemExit(int)"><B>fireSystemExit(int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#fireVetoableAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><B>fireVetoableAlignmentEvent(VetoableAlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#fireVetoableAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><B>fireVetoableAlignmentEvent(VetoableAlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>Notifies the vetoable listeners of a MSA vetoable event.
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireVetoableSequenceEvent(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>fireVetoableSequenceEvent(VetoableSequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#fireVetoableSequenceEvent(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>fireVetoableSequenceEvent(VetoableSequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>This function fires the vetoable event to the vetoable listeners.
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#firstElement()"><B>firstElement()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#forceOptionable()"><B>forceOptionable()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#forceOptionable()"><B>forceOptionable()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Force the setting the optionable status now.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>FormattedDocument</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html">FormattedDocument</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#FormattedDocument(java.text.Format)"><B>FormattedDocument(Format)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html">FormattedDocument</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_G_"><!-- --></A><H2>
+<B>G</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html#gap"><B>gap</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>Gap</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A>.<DD>Gap.java
+
+
+ Created: Wed Mar 1 19:35:57 2000<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html#GAP"><B>GAP</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html#GAPDELETE"><B>GAPDELETE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html#GAPINSERT"><B>GAPINSERT</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html"><B>GappableSequenceTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html">GappableSequenceTest</A>.<DD>GappableSequenceTest.java
+
+
+ Created: Tue Mar 7 13:45:10 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html#GappableSequenceTest()"><B>GappableSequenceTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html">GappableSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A>.<DD>GappedComplexSequence.java
+
+ Place holder type interface.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A> - interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>.<DD>GappedSequence.java
+
+
+ Created: Wed Mar 1 18:28:44 2000<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html"><B>GappedSequenceCharacterIterator</B></A> - class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A>.<DD>GappedSequenceCharacterIterator.java
+
+
+ Created: Mon Feb 5 14:06:28 2001<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#GappedSequenceCharacterIterator(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>GappedSequenceCharacterIterator(GappedSequence)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html"><B>GappedSequenceGroup</B></A> - interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>.<DD>GappedSequenceGroup.java
+
+ An extension of SequenceGroup with some methods to return
+ GappedSequences.<DT><A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html"><B>GappedSequenceSearch</B></A> - class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html">GappedSequenceSearch</A>.<DD>SequenceSearch.java
+
+ Searches through a SequenceAlignment specified on the command line for
+ all occurrences of the given regexp.<DT><A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html#GappedSequenceSearch()"><B>GappedSequenceSearch()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html">GappedSequenceSearch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html"><B>GappedSequenceTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html">GappedSequenceTest</A>.<DD>GappedSequenceTest.java
+
+
+ Created: Wed Jun 7 16:18:11 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html#GappedSequenceTest()"><B>GappedSequenceTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html">GappedSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#generateColorMap()"><B>generateColorMap()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html">CinemaTestLaunch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#generateMsa()"><B>generateMsa()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html">CinemaTestLaunch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#genericEnd()"><B>genericEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html"><B>GenericModuleIdentifier</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html">GenericModuleIdentifier</A>.<DD>GenericModuleIdentifier.java
+
+
+ Created: Mon May 15 16:02:45 2000<DT><A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html#GenericModuleIdentifier(java.lang.String, java.lang.String, boolean)"><B>GenericModuleIdentifier(String, String, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html">GenericModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#get(int)"><B>get(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#get(int)"><B>get(int)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Returns the module identifier at a given index.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#get(int)"><B>get(int)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Returns the module at a given index.
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#get(int)"><B>get(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getAboutText()"><B>getAboutText()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getAccession()"><B>getAccession()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getActions()"><B>getActions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getActions()"><B>getActions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getActions()"><B>getActions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()"><B>getActions()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#getActions()"><B>getActions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getActions()"><B>getActions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getActions()"><B>getActions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>Supplies the action for the menu system/whatever else wishes to
+ invoke this modules action.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><B>getActions(CinemaAlignmentFrame)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><B>getActions(CinemaAlignmentFrame)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><B>getActions(CinemaAlignmentFrame)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html">CinemaResizeElements</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><B>getActions(CinemaAlignmentFrame)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html">CinemaRegexp</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html#getActions(uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui)"><B>getActions(CinemaCoreGui)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html">CinemaSharedQuitExit</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getAlignment()"><B>getAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#getAlignment()"><B>getAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()"><B>getAlignmentFrame()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getAlignmentFrame()"><B>getAlignmentFrame()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getAlignmentSelectionModel()"><B>getAlignmentSelectionModel()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getAlignmentSelectionModel()"><B>getAlignmentSelectionModel()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getAlignmentSelectionRenderer()"><B>getAlignmentSelectionRenderer()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html#getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>getAlignmentViewerCellRendererComponent(JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html">DefaultAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html#getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>getAlignmentViewerCellRendererComponent(JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A>
+<DD>This method should be able to cope with null values for element
+ which will be passed if we are off the front or the end of the sequence
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html#getAll()"><B>getAll()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html#getAll()"><B>getAll()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#getAll()"><B>getAll()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html#getAllColorGenerator()"><B>getAllColorGenerator()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#getAllColorList()"><B>getAllColorList()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)"><B>getAllElements(Class)</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getAllGroups()"><B>getAllGroups()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)"><B>getAllIdentifiers(Class)</B></A> -
+Static method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getAllMetaData()"><B>getAllMetaData()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html#getAllSequenceElements(java.lang.Class)"><B>getAllSequenceElements(Class)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A>
+<DD>Returns all the elements.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getAnchorManager()"><B>getAnchorManager()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getAuthorString()"><B>getAuthorString()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getAuthorURLs()"><B>getAuthorURLs()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getAvailableParsers()"><B>getAvailableParsers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getAvailableParsers()"><B>getAvailableParsers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#getBottomLeft()"><B>getBottomLeft()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html#getBounds()"><B>getBounds()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A>
+<DD>Returns the boundaries of the shape used to identify a region in
+ a sequence alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getBounds()"><B>getBounds()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Returns the rectangle which defines the boundries of the region
+ defined by this object.
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html#getCalculator(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>getCalculator(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getCalculatorInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>getCalculatorInstance(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#getCalculatorName()"><B>getCalculatorName()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getCalculatorName()"><B>getCalculatorName()</B></A> -
+Method in interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getCellBounds(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getCellBounds(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getCellBounds(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Rectangle)"><B>getCellBounds(SequenceAlignmentPoint, Rectangle)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellHeight()"><B>getCellHeight()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellRenderer()"><B>getCellRenderer()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#getCellsSquare()"><B>getCellsSquare()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellWidth()"><B>getCellWidth()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getCheckSum()"><B>getCheckSum()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>Returns a checksum value.
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#getChildNodes()"><B>getChildNodes()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html#getClassName()"><B>getClassName()</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>
+<DD>Returns the string of the class name.
+<DT><A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html#getClassName()"><B>getClassName()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html">GenericModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()"><B>getClassName()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#getColdToHotColorList()"><B>getColdToHotColorList()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#getColor()"><B>getColor()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#getColorAt(int)"><B>getColorAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html">SingleColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html">IndividualElementColorMap</A>
+<DD>Returns the color for an element at a specific position in the
+ alignment.
+<DT><A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html">DoubleArrayColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getColorAt(SequenceAlignment, Element, SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>
+<DD>Returns the Color at a specific position in the alignment.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getColorFactory()"><B>getColorFactory()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getColorMap()"><B>getColorMap()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getColorMap()"><B>getColorMap()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getColorMap()"><B>getColorMap()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>Returns the current color map.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getColorMapIterator()"><B>getColorMapIterator()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html">NullColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html">WhiteColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html">GrayScaleVariance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#getColorMapName()"><B>getColorMapName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#getColumn()"><B>getColumn()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html#getCommandLineArguments()"><B>getCommandLineArguments()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html">Cinema</A>
+<DD>Returns the arguments supplied to Cinema on the command line, and
+ stored in the 'main' function.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#getComplexElement(uk.ac.man.bioinf.sequence.Residue)"><B>getComplexElement(Residue)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#getComplexElement(uk.ac.man.bioinf.sequence.Residue)"><B>getComplexElement(Residue)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getComplexElementAt(int)"><B>getComplexElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getComplexElementAt(int)"><B>getComplexElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAt(int)"><B>getComplexElementAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAtAsChar(int)"><B>getComplexElementAtAsChar(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>
+<DD>Representing a ComplexElement as a char is not a simple task.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexElementAtAsChar(int)"><B>getComplexElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexSequenceAsChars()"><B>getComplexSequenceAsChars()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexSequenceAsChars()"><B>getComplexSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getComplexSequenceAsString(uk.ac.man.bioinf.sequence.complex.ComplexSequence)"><B>getComplexSequenceAsString(ComplexSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexSequenceTypeException(uk.ac.man.bioinf.sequence.Element)"><B>getComplexSequenceTypeException(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexType()"><B>getComplexType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#getConcreteIdentifier()"><B>getConcreteIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#getConfig()"><B>getConfig()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#getConfig()"><B>getConfig()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>Returns an object representing the configuration of the module.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html#getConfig()"><B>getConfig()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html">DefaultModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getConfig(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getConfig(ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Returns the config object a given module
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getConfig(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()"><B>getConfigProperties()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()"><B>getConfigTree()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getConsensus()"><B>getConsensus()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getConsensusCalculator()"><B>getConsensusCalculator()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#getConsensusCalculator()"><B>getConsensusCalculator()</B></A> -
+Method in interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#getConsensusCalculatorName()"><B>getConsensusCalculatorName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getConsensusCalculatorName()"><B>getConsensusCalculatorName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getConsensusCalculatorName()"><B>getConsensusCalculatorName()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><B>getConsensusInstance(ConsensusSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html">InstancePerAlignmentColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html">NullColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html">WhiteColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html">GrayScaleVariance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>
+<DD>Returns an instance of this type for this consensus sequence
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getConsensusInstance(ConsensusSequence, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getConsensusModule()"><B>getConsensusModule()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#getContents()"><B>getContents()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#getContext()"><B>getContext()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#getContext()"><B>getContext()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>Returns the modules context.
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#getCurrentConsensus()"><B>getCurrentConsensus()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getCurrentConsensus()"><B>getCurrentConsensus()</B></A> -
+Method in interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#getCurrentlySelectedIndex()"><B>getCurrentlySelectedIndex()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#getCurrentlySelectedName()"><B>getCurrentlySelectedName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#getCurrentlySelectedRect()"><B>getCurrentlySelectedRect()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getCurrentSelection()"><B>getCurrentSelection()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getCurrentSelection()"><B>getCurrentSelection()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getCurrentSelection()"><B>getCurrentSelection()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getCurrentSelection()"><B>getCurrentSelection()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Returns the current selection or null if there is no
+ selection.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getCurrentSelectionName()"><B>getCurrentSelectionName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCursorModel()"><B>getCursorModel()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html#getDatabaseName()"><B>getDatabaseName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html">SwissProtIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getDatabaseName()"><B>getDatabaseName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getDecimalFieldValue(java.lang.String)"><B>getDecimalFieldValue(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getDefaultColorMapMetaData()"><B>getDefaultColorMapMetaData()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html#getDefaultInstance()"><B>getDefaultInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#getDefaultInvokerInternalQueue()"><B>getDefaultInvokerInternalQueue()</B></A> -
+Static method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getDefaultMetaData()"><B>getDefaultMetaData()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getDefaultOptionHandler()"><B>getDefaultOptionHandler()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getDefaultOptionHandler()"><B>getDefaultOptionHandler()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#getDefaultQueue()"><B>getDefaultQueue()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html">InvokerThreadManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html#getDescription()"><B>getDescription()</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html#getDescription()"><B>getDescription()</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A>
+<DD>Returns the description of this alignment output parser, and
+ should be human readable/understandable.
+<DT><A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html#getDescription()"><B>getDescription()</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>
+<DD>Returns the description of this alignment parser, and should be
+ human readable/understandable.
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#getDescription()"><B>getDescription()</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A>
+<DD>Returns that this is a PIR/NBRF protein sequence parser.
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html#getDescription()"><B>getDescription()</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html">MotProteinParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#getDescription()"><B>getDescription()</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html">FastaSequenceParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html#getDNASequence(char[])"><B>getDNASequence(char[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>
+<DD>Create a Sequence representing a DNA sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html#getDNASequence(java.lang.String)"><B>getDNASequence(String)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>
+<DD>Create a Sequence representing a DNA sequence.
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">AlignmentToListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns an element at a given location.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getElementAt(int)"><B>getElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)"><B>getElementAtAsChar(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns the character of an target element.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getElementAtAsChar(int)"><B>getElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#getElementAtAsChar(int)"><B>getElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getElementAtAsChar(int)"><B>getElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementAtAsChar(int)"><B>getElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#getElementAtRow(int)"><B>getElementAtRow(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>Get the element for this column at the given row.
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)"><B>getElementForInt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>The inverse of the method getIntForElement.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getElementForInt(int)"><B>getElementForInt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getElementForInt(int)"><B>getElementForInt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getElementForInt(int)"><B>getElementForInt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#getElements()"><B>getElements()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns all the elements available in this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getElements()"><B>getElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()"><B>getElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getElements()"><B>getElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><B>getElementsAsGappedSequence(Element[], SequenceType)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>Returns a GappedSequence with the Elements in the array, which
+ can included gaps.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><B>getElementsAsGappedSequence(Element[], SequenceType)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><B>getElementsAsGappedSequence(Element[], SequenceType)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>getElementsAsGappedSequence(Element[], SequenceType, Identifier)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>Returns a GappedSequence with the Elements in the array, which
+ can included gaps.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>getElementsAsGappedSequence(Element[], SequenceType, Identifier)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>getElementsAsGappedSequence(Element[], SequenceType, Identifier)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><B>getElementsAsSequence(Element[], SequenceType)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>getElementsAsSequence(Element[], SequenceType, Identifier)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsString(uk.ac.man.bioinf.sequence.Element[])"><B>getElementsAsString(Element[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getEnd()"><B>getEnd()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A>
+<DD>Returns the end location of the event.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html#getEvent()"><B>getEvent()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>
+<DD>Returns the multiple sequence event that spawned the veto.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html#getEvent()"><B>getEvent()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>
+<DD>Returns the sequence event that the veto objected to
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html#getException()"><B>getException()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html">InvokerInternalEventQueueException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getExceptionHandler()"><B>getExceptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getExceptionHandler()"><B>getExceptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>Returns the parser exception handler.
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getExceptionHandler()"><B>getExceptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#getExpcetedSequenceType()"><B>getExpcetedSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>
+<DD>Returns the expected sequence type.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getFastCellRenderer()"><B>getFastCellRenderer()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html#getFile()"><B>getFile()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html">FileSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getFile(java.lang.String)"><B>getFile(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is file.<fileDescriptor> value should be path to the image
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#getFormat()"><B>getFormat()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html">FormattedDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#getFormat()"><B>getFormat()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()"><B>getFrame()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getFrame()"><B>getFrame()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html#getFullName()"><B>getFullName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html#getFullName()"><B>getFullName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#getFullName()"><B>getFullName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGapModelForElements(uk.ac.man.bioinf.sequence.Element[])"><B>getGapModelForElements(Element[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedElementAt(int)"><B>getGappedElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)"><B>getGappedElementAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedElementAt(int)"><B>getGappedElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedElementAt(int)"><B>getGappedElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedElementAt(int)"><B>getGappedElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)"><B>getGappedElementAtAsChar(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedElementAtAsChar(int)"><B>getGappedElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#getGappedElementAtAsChar(int)"><B>getGappedElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedElementAtAsChar(int)"><B>getGappedElementAtAsChar(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedLength()"><B>getGappedLength()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedLength()"><B>getGappedLength()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>Returns the gapped length of this sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedLength()"><B>getGappedLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedLength()"><B>getGappedLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedLength()"><B>getGappedLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedPositionOf(int)"><B>getGappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedPositionOf(int)"><B>getGappedPositionOf(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>Translate between the gapped index, and the ungapped index
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedPositionOf(int)"><B>getGappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedPositionOf(int)"><B>getGappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedPositionOf(int)"><B>getGappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsChars()"><B>getGappedSequenceAsChars()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedSequenceAsChars()"><B>getGappedSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#getGappedSequenceAsChars()"><B>getGappedSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedSequenceAsChars()"><B>getGappedSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedSequenceAsElements()"><B>getGappedSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsElements()"><B>getGappedSequenceAsElements()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedSequenceAsElements()"><B>getGappedSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedSequenceAsElements()"><B>getGappedSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedSequenceAsElements()"><B>getGappedSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getGappedSequenceAsString(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getGappedSequenceAsString(GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getGappedSequenceAt(int)"><B>getGappedSequenceAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#getGappedSequenceIndexException(int)"><B>getGappedSequenceIndexException(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html#getGappedSequences()"><B>getGappedSequences()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>
+<DD>Return all the sequences in this group as a GappedSequence
+ array.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#getGappedSequences()"><B>getGappedSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedSubSequence(int, int)"><B>getGappedSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSubSequence(int, int)"><B>getGappedSubSequence(int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedSubSequence(int, int)"><B>getGappedSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedSubSequence(int, int)"><B>getGappedSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedSubSequence(int, int)"><B>getGappedSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getGappedSubSequenceAsString(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int, int)"><B>getGappedSubSequenceAsString(GappedSequence, int, int)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#getGray50List()"><B>getGray50List()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getGroupByName(java.lang.String)"><B>getGroupByName(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>Returns group with name or null
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getGroupContaining(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getGroupContaining(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getGroupManager()"><B>getGroupManager()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getHeight()"><B>getHeight()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#getHeight()"><B>getHeight()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Returns the height of this dimension.
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getHelpURL(java.lang.String)"><B>getHelpURL(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is helpURL.<helpURLName>
+<DT><A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html#getHelpURL(java.lang.String)"><B>getHelpURL(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#getHotToColdColorList()"><B>getHotToColdColorList()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#getID()"><B>getID()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html">NoSuchRequiredModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>Returns the modules identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>Returns a module identifier for this module.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html">DefaultModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()"><B>getIdentifier()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getImageURL(java.lang.String)"><B>getImageURL(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is image.<imageName> value should be path to the image
+<DT><A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html#getImageURL(java.lang.String)"><B>getImageURL(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#getIndex()"><B>getIndex()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getInset(int)"><B>getInset(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Returns the inset of sequence within the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getInset(int)"><B>getInset(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getInset(int)"><B>getInset(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns the inset of a particular sequence in the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getInset(int)"><B>getInset(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html">NullOptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html#getInstance()"><B>getInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>getInstance(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html">InstancePerAlignmentColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>getInstance(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>getInstance(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>getInstance(SequenceAlignment)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html">NullColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html">WhiteColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html">GrayScaleVariance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>getInstance(SequenceAlignment, JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getIntegerFieldValue(java.lang.String)"><B>getIntegerFieldValue(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#getInternalThreadedColorMap()"><B>getInternalThreadedColorMap()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)"><B>getIntForElement(Element)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>This method is present as a performance enhancement.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)"><B>getIntForElement(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)"><B>getIntForElement(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)"><B>getIntForElement(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getInvokerInternalQueue()"><B>getInvokerInternalQueue()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#getJList()"><B>getJList()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html">SwappingListBasicUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()"><B>getJMenuBar()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getJMenuBar()"><B>getJMenuBar()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#getLastPriorityRun()"><B>getLastPriorityRun()</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A>
+<DD>The priority of the last listener which this class attempted to
+ inform of a system event.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getLastSequence()"><B>getLastSequence()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#getLastSequence()"><B>getLastSequence()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getLength()"><B>getLength()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns the length of the sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getLength()"><B>getLength()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Returns the length of the alignment (i.e: the longest sequence).
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns the length of the multiple sequence alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>
+<DD>Returns the end location of the event.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getLength()"><B>getLength()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html#getLightColorGenerator()"><B>getLightColorGenerator()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#getLightColorList()"><B>getLightColorList()</B></A> -
+Static method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html#getListCellRendererComponent(javax.swing.JList, java.lang.Object, int, boolean, boolean)"><B>getListCellRendererComponent(JList, Object, int, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html">AlignmentToListCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getLoadStream()"><B>getLoadStream()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html#getLoadStream()"><B>getLoadStream()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html">FileSaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getLocation()"><B>getLocation()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Returns the location of the rectangle
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#getLocation()"><B>getLocation()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Returns the location in the sequence alignment, represented by
+ this object.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getMainPanel()"><B>getMainPanel()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getMaintainerURL()"><B>getMaintainerURL()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#getMainWindow()"><B>getMainWindow()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#getMark()"><B>getMark()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>
+<DD>Returns the position of mark
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getMark()"><B>getMark()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#getMark()"><B>getMark()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getMaximumSize()"><B>getMaximumSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getMaximumSize()"><B>getMaximumSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getMenuSystem()"><B>getMenuSystem()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getMessageString(java.lang.String)"><B>getMessageString(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is message.<messageName>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getMetaData(uk.ac.man.bioinf.gui.color.ColorMap)"><B>getMetaData(ColorMap)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>Returns a meta data object for the given ColorMap.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getMetaData(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>getMetaData(ConsensusCalculator)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getMetaData(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><B>getMetaData(ConsensusSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getMetaData(java.lang.String)"><B>getMetaData(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getMetaData(java.lang.String)"><B>getMetaData(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getMetaDataInstance()"><B>getMetaDataInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getMinimumSize()"><B>getMinimumSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getMinimumSize()"><B>getMinimumSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html#getModification(java.lang.String)"><B>getModification(String)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html">ModificationFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getModifications()"><B>getModifications()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#getModifications()"><B>getModifications()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#getModifications()"><B>getModifications()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>
+<DD>Gets all of the Modifications which are allowable in this
+ sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html#getModifications()"><B>getModifications()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#getModifications()"><B>getModifications()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet()"><B>getModificationSet()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet()"><B>getModificationSet()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet()"><B>getModificationSet()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)"><B>getModificationSet(Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)"><B>getModificationSet(Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)"><B>getModificationSet(Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])"><B>getModificationSet(Modification[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])"><B>getModificationSet(Modification[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])"><B>getModificationSet(Modification[])</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)"><B>getModificationSet(Modification[], Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)"><B>getModificationSet(Modification[], Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)"><B>getModificationSet(Modification[], Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getModifierType(java.lang.String)"><B>getModifierType(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#getModule()"><B>getModule()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#getModule()"><B>getModule()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>Returns the associated module for this context.
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getModule(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getModule(ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Returns the module, given the module identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getModule(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>Returns a module by interfacing with the ModuleHandlerFactory.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getModule(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#getModuleData()"><B>getModuleData()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getModuleDTDAsResource()"><B>getModuleDTDAsResource()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#getModuleFactory()"><B>getModuleFactory()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html#getModuleName()"><B>getModuleName()</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>
+<DD>Returns the name of the module being defined.
+<DT><A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html#getModuleName()"><B>getModuleName()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html">GenericModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()"><B>getModuleName()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html">SingleColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html">IndividualElementColorMap</A>
+<DD>Returns the name of this color map.
+<DT><A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html">DoubleArrayColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html#getName()"><B>getName()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>
+<DD>Returns the name of this colour scheme.
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#getName()"><B>getName()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns the human readable form of this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getName()"><B>getName()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html#getName()"><B>getName()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#getNamedThread(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, java.lang.String)"><B>getNamedThread(SystemEventProducer, String)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html">InvokerThreadManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getNewInvokerInternalQueue()"><B>getNewInvokerInternalQueue()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getNumberGapsDownstreamFrom(int, uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getNumberGapsDownstreamFrom(int, GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>Returns the number of gaps downstream from a given index in the
+ given sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getNumberGapsUpstreamFrom(int, uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getNumberGapsUpstreamFrom(int, GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>Returns the number of gaps upstream from a given index in the
+ given sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html#getNumberOfSequences()"><B>getNumberOfSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html">SingleSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getNumberSelections()"><B>getNumberSelections()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getNumberSelections()"><B>getNumberSelections()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getNumberSelections()"><B>getNumberSelections()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getNumberSelections()"><B>getNumberSelections()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Get the number of selections.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getNumberSequences()"><B>getNumberSequences()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Returns the total number of sequences in the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getNumberSequences()"><B>getNumberSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getNumberSequences()"><B>getNumberSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns the total number of sequences in the multiple sequence alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#getNumberSequences()"><B>getNumberSequences()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Return the number of sequences in this group.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getNumberSequences()"><B>getNumberSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getNumberSequences()"><B>getNumberSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#getOneAtATime()"><B>getOneAtATime()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>Get the value of oneAtATime.
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html#getOption()"><B>getOption()</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionGroupName()"><B>getOptionGroupName()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>
+<DD>This string is used as an identifier for the groups
+ of options.
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getOptionGroupName()"><B>getOptionGroupName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptionGroupName()"><B>getOptionGroupName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Subclasses must provide this, either on a class or instance basis
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#getOptionHandler()"><B>getOptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#getOptionHandler()"><B>getOptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionHandler()"><B>getOptionHandler()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>
+<DD>Get the value of OptionHandler.
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getOptionHandler()"><B>getOptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptionHandler()"><B>getOptionHandler()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Implementation of the Optionable interface
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getOptions()"><B>getOptions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptions()"><B>getOptions()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>
+<DD>This method provides the current state of object as a map
+ of objects
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getOptions()"><B>getOptions()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptions()"><B>getOptions()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>An implementation of the Optionable interface.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html#getPage(java.net.URL)"><B>getPage(URL)</B></A> -
+Static method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html">PopUpHtmlDisplay</A>
+<DD>try to open the URL and get the page
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#getParameter()"><B>getParameter()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>Get the parameter
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#getParameter(int)"><B>getParameter(int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>Get the parameter specified by the given
+ index.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getParser(java.lang.String)"><B>getParser(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getParser(java.lang.String)"><B>getParser(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getParserDescription(java.lang.String)"><B>getParserDescription(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getParserDescription(java.lang.String)"><B>getParserDescription(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#getParserExceptions()"><B>getParserExceptions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A>
+<DD>Return the stored exceptions, so that they can be displayed all
+ together.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#getParserExceptions()"><B>getParserExceptions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A>
+<DD>Return the stored exceptions, so that they can be displayed all
+ together.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#getPassword()"><B>getPassword()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#getPasswordPane()"><B>getPasswordPane()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#getPoint()"><B>getPoint()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>
+<DD>Returns the position of point
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPoint()"><B>getPoint()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#getPoint()"><B>getPoint()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPointAtSequencePoint(int, int)"><B>getPointAtSequencePoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getPointAtSequencePoint(int, int)"><B>getPointAtSequencePoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getPointAtSequencePoint(int, int)"><B>getPointAtSequencePoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getPointAtSequencePoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getPointAtSequencePoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getPointForSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getPointForSequence(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#getPopupMenu()"><B>getPopupMenu()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#getPosition()"><B>getPosition()</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>Returns the integer position in the sequence that caused the
+ exception.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getPreferredHeight()"><B>getPreferredHeight()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPreferredScrollableViewportSize()"><B>getPreferredScrollableViewportSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPreferredSize()"><B>getPreferredSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getPreferredSize()"><B>getPreferredSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#getPreferredSize(javax.swing.JComponent)"><B>getPreferredSize(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getPreferredWidthPerBase()"><B>getPreferredWidthPerBase()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getProjectURL()"><B>getProjectURL()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html#getProteinSequence(char[])"><B>getProteinSequence(char[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>
+<DD>Create a Sequence representing a protein sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html#getProteinSequence(java.lang.String)"><B>getProteinSequence(String)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>
+<DD>Create a Sequence representing a protein sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#getReader()"><B>getReader()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectangleAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectangleAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectangleAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectangleAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Get the first selection rectangle which surrounds the point, or
+ null if there is not one.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getRectangleForSequenceRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>getRectangleForSequenceRectangle(SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectanglesAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectanglesAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectanglesAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>getRectanglesAtPoint(SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Get all selection rectangles which surround this point, or null
+ if there is not one
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html">CinemaMenuSystem</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()"><B>getRequiredIdentifiers()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>Returns the module identifiers for the required modules.
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#getRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getRequiredModule(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#getRequiredModules()"><B>getRequiredModules()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#getRequiredModules()"><B>getRequiredModules()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#getRequiredModules()"><B>getRequiredModules()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>Returns the required modules for this module (ie: the modules
+ that are necessary in order for this module to function).
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getRequiredModules(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getRequiredModules(ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Returns the modules required by the given module.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getRequiredModules(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#getResidue()"><B>getResidue()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html#getResidue()"><B>getResidue()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getResiduesAsComplexElements(uk.ac.man.bioinf.sequence.Residue[])"><B>getResiduesAsComplexElements(Residue[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getResource(java.lang.String)"><B>getResource(String)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#getResourceAdapter()"><B>getResourceAdapter()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRowHeaders()"><B>getRowHeaders()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRowHeaders()"><B>getRowHeaders()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getRowHeaders()"><B>getRowHeaders()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRuler()"><B>getRuler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRuler()"><B>getRuler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getRuler()"><B>getRuler()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRulerPanel()"><B>getRulerPanel()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRulerPanel()"><B>getRulerPanel()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getRulerPanel()"><B>getRulerPanel()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getSaveStream()"><B>getSaveStream()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html#getSaveStream()"><B>getSaveStream()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html">FileSaveableOptions</A>
+<DD>These were originally going to be abstract but you cant make
+ abstract static methods.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableBlockIncrement(java.awt.Rectangle, int, int)"><B>getScrollableBlockIncrement(Rectangle, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableTracksViewportHeight()"><B>getScrollableTracksViewportHeight()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableTracksViewportWidth()"><B>getScrollableTracksViewportWidth()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableUnitIncrement(java.awt.Rectangle, int, int)"><B>getScrollableUnitIncrement(Rectangle, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getScrollPane()"><B>getScrollPane()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getScrollPane()"><B>getScrollPane()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getScrollPane()"><B>getScrollPane()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getSelectedObjects()"><B>getSelectedObjects()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html#getSelectedSequence()"><B>getSelectedSequence()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html">ButtonViewerPopupMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getSelectionAt(int)"><B>getSelectionAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getSelectionAt(int)"><B>getSelectionAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getSelectionAt(int)"><B>getSelectionAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getSelectionAt(int)"><B>getSelectionAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Gets the given selection.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getSelectionForName(java.lang.String)"><B>getSelectionForName(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSelectionModel()"><B>getSelectionModel()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getSelectionNameIterator()"><B>getSelectionNameIterator()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#getSelectionRectangle()"><B>getSelectionRectangle()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#getSequence()"><B>getSequence()</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>Returns the sequence that caused the exception.
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#getSequenceAlignment()"><B>getSequenceAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getSequenceAlignment()"><B>getSequenceAlignment()</B></A> -
+Method in interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getSequenceAlignment()"><B>getSequenceAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getSequenceAlignment()"><B>getSequenceAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSequenceAlignment()"><B>getSequenceAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getSequenceAlignment()"><B>getSequenceAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getSequenceAlignmentRectangleAtRectangle(java.awt.Rectangle)"><B>getSequenceAlignmentRectangleAtRectangle(Rectangle)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()"><B>getSequenceAsChars()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns the sequence as an array of characters.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getSequenceAsChars()"><B>getSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceAsChars()"><B>getSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSequenceAsChars()"><B>getSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSequenceAsChars()"><B>getSequenceAsChars()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSequenceAsComplexElements()"><B>getSequenceAsComplexElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getSequenceAsComplexElements()"><B>getSequenceAsComplexElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns the sequence as an array of elements.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getSequenceAsElements()"><B>getSequenceAsElements()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getSequenceAsString(uk.ac.man.bioinf.sequence.Sequence)"><B>getSequenceAsString(Sequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceAt(int)"><B>getSequenceAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Provides the sequence at a particular location in the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSequenceAt(int)"><B>getSequenceAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSequenceAt(int)"><B>getSequenceAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns the sequence, given a specific location in the MSA.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequenceAt(int)"><B>getSequenceAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getSequenceAt(int)"><B>getSequenceAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getSequenceColor(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getSequenceIndex(GappedSequence)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Returns the index in the alignment of a provided sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getSequenceIndex(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getSequenceIndex(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns the location of a sequence, in the multiple sequence alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>getSequenceIndex(GappedSequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceIndexException(int)"><B>getSequenceIndexException(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSequencePointAtPoint(int, int)"><B>getSequencePointAtPoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getSequencePointAtPoint(int, int)"><B>getSequencePointAtPoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(int, int)"><B>getSequencePointAtPoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSequencePointAtPoint(java.awt.Point)"><B>getSequencePointAtPoint(Point)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(java.awt.Point)"><B>getSequencePointAtPoint(Point)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#getSequences()"><B>getSequences()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Get all the sequences in this group.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequences()"><B>getSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getSequences()"><B>getSequences()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns the type of sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Returns the sequence type of the alignment (e.g: protein sequences).
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns the sequence type for the alignment (e.g: Protien Sequence).
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequenceType()"><B>getSequenceType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceTypeException(uk.ac.man.bioinf.sequence.Element)"><B>getSequenceTypeException(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html#getSharedModuleInstance(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>getSharedModuleInstance(ModuleIdentifier)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html">Cinema</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html#getSingleSequence()"><B>getSingleSequence()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html">SingleSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getSize()"><B>getSize()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#getSize()"><B>getSize()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">AlignmentToListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#getSize()"><B>getSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>Everything that follows this is just a straight copy from
+ the default list model
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getSize()"><B>getSize()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Returns the size of the rectangle.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#getSize()"><B>getSize()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Returns the dimensions of this dimension (que????).
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)"><B>getSize(Class)</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#getSlowReturn()"><B>getSlowReturn()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#getSource()"><B>getSource()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>Get the source
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#getSource()"><B>getSource()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#getSource()"><B>getSource()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html#getSource()"><B>getSource()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>
+<DD>This returns the source of the sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#getSource()"><B>getSource()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getStart()"><B>getStart()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A>
+<DD>Returns the start location of the event.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getStart()"><B>getStart()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>
+<DD>Returns the start location of the event.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getStatusBar()"><B>getStatusBar()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getStatusBar()"><B>getStatusBar()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#getStringData()"><B>getStringData()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(int, int, int, int)"><B>getSubAlignment(int, int, int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Returns a sub-alignment, given the exact location in this alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSubAlignment(int, int, int, int)"><B>getSubAlignment(int, int, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSubAlignment(int, int, int, int)"><B>getSubAlignment(int, int, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Returns a sub-alignment, given the exact location in this alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSubAlignment(int, int, int, int)"><B>getSubAlignment(int, int, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>getSubAlignment(SequenceAlignmentRectangle)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>getSubAlignment(SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>getSubAlignment(SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>getSubAlignment(SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#getSubList(int, int)"><B>getSubList(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)"><B>getSubSequence(int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>
+<DD>Returns a sub-sequence from the current sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html#getSubSequence(int, int)"><B>getSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html">EmptySequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html#getSubSequence(int, int)"><B>getSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSubSequence(int, int)"><B>getSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSubSequence(int, int)"><B>getSubSequence(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#getSubSequenceAsString(uk.ac.man.bioinf.sequence.Sequence, int, int)"><B>getSubSequenceAsString(Sequence, int, int)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html#getSystemEvent()"><B>getSystemEvent()</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getTextFieldValue(java.lang.String)"><B>getTextFieldValue(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getTextString(java.lang.String)"><B>getTextString(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is string.<descriptor> value should be a String
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#getThreeLetter()"><B>getThreeLetter()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#getThrowable()"><B>getThrowable()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html">ConsensusIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html">URLSequenceSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">SimpleSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html#getTitle()"><B>getTitle()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>
+<DD>Get the human readable name for this SequenceSource
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html">SimpleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html#getTitle()"><B>getTitle()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A>
+<DD>Get the human readable name for this SequenceSource
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html">NoSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html#getTitle()"><B>getTitle()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>
+<DD>Gets a human readable title for the Sequence
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html">FileSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getTitle()"><B>getTitle()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getToolTip(java.lang.String)"><B>getToolTip(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is tooltip.<tooltipName>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#getTopLeft()"><B>getTopLeft()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getType()"><B>getType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A>
+<DD>Returns the multiple sequence event type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getType()"><B>getType()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>
+<DD>Returns the seqyence event type.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getUIClassID()"><B>getUIClassID()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getUIClassID()"><B>getUIClassID()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getUngappedPositionOf(int)"><B>getUngappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getUngappedPositionOf(int)"><B>getUngappedPositionOf(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>Translate between the gapped position and the ungapped
+ position.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getUngappedPositionOf(int)"><B>getUngappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getUngappedPositionOf(int)"><B>getUngappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getUngappedPositionOf(int)"><B>getUngappedPositionOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html#getURL()"><B>getURL()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html">URLSequenceSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#getURL(java.lang.String)"><B>getURL(String)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>property is url.<URLDescriptor> value should be a URL
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getUserExtensions()"><B>getUserExtensions()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#getUserName()"><B>getUserName()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getUserPersist()"><B>getUserPersist()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#getValue()"><B>getValue()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">WholeNumberField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html#getValue()"><B>getValue()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html#getValue()"><B>getValue()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">DecimalField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getVariance()"><B>getVariance()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html">CinemaMenuSystem</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html">CinemaGo</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html">CinemaSlaveViewerModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html">CinemaStatusInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html">CinemaResizeElements</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html">CinemaRegexp</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html">CinemaMenuBuilder</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html">CinemaSplash</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html">CinemaSharedQuitExit</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html">FileSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#getVersion()"><B>getVersion()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>Returns the version of this module.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getVersionNumber()"><B>getVersionNumber()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getViewer()"><B>getViewer()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getViewer()"><B>getViewer()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getViewer()"><B>getViewer()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#getViewer()"><B>getViewer()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A>
+<DD>Returns the <code>JAlignmentViewer</code> that caused the
+ exception, or null if the exception came from elsewhere.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getVisibleSequenceRectangle()"><B>getVisibleSequenceRectangle()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getWidth()"><B>getWidth()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#getWidth()"><B>getWidth()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Returns the width of this dimension.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getX()"><B>getX()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#getX()"><B>getX()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Returns the X index of the point.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html#getXMLParser()"><B>getXMLParser()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html">CinemaXMLParserFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html#getXMLParser()"><B>getXMLParser()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html#getXMLParser()"><B>getXMLParser()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html">DefaultXMLParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#getXMLParserClass()"><B>getXMLParserClass()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#getXMLParserClass()"><B>getXMLParserClass()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getY()"><B>getY()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#getY()"><B>getY()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Returns the Y index of the point.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLUORGLN"><B>GLUORGLN</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLUTAMICACID"><B>GLUTAMICACID</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLUTAMINE"><B>GLUTAMINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLYCINE"><B>GLYCINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>GrayScaleVariance</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html">GrayScaleVariance</A>.<DD>GrayScaleVariance.java
+
+
+ Created: Fri Nov 30 13:58:29 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#GrayScaleVariance()"><B>GrayScaleVariance()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html">GrayScaleVariance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#GREATER_THAN"><B>GREATER_THAN</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html"><B>GroupSequenceAlignment</B></A> - class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>.<DD>GroupSequenceAlignment.java
+
+ This is a sequence group which also reflects a sequence
+ alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#GroupSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>GroupSequenceAlignment(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>Start an empty sequence group associated with the given sequence
+ alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#GroupSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.util.IntArrayList)"><B>GroupSequenceAlignment(SequenceAlignment, IntArrayList)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>Starts an Sequence group with the sequences given in the IntArrayList
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#groupsName"><B>groupsName</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#groupsOrder"><B>groupsOrder</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html#GUANINE"><B>GUANINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html#GUANINE"><B>GUANINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_H_"><!-- --></A><H2>
+<B>H</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)"><B>handleException(ParserException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html">FileSequenceParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)"><B>handleException(ParserException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html">FileSequenceInputParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)"><B>handleException(ParserException)</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>
+<DD>Handles exceptions thrown by a sequence parser.
+<DT><A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)"><B>handleException(ParserException)</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html">NullParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)"><B>handleException(ParserException)</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html">DefaultParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html#handleException(java.lang.Throwable)"><B>handleException(Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html">ExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(java.lang.ClassNotFoundException)"><B>handleLoadException(ClassNotFoundException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.lang.ClassNotFoundException)"><B>handleLoadException(ClassNotFoundException)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>
+<DD>ClassNotFoundException can occur when reading data from the
+ stream for a data type that does not exist.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(java.lang.Exception)"><B>handleLoadException(Exception)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.lang.Exception)"><B>handleLoadException(Exception)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>
+<DD>Handle an exception occurring during the loading of options.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(java.io.IOException)"><B>handleLoadException(IOException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.io.IOException)"><B>handleLoadException(IOException)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>
+<DD>Signalled if some unknown IOException occurs
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)"><B>handleLoadException(OptionableSourceNotFoundException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)"><B>handleLoadException(OptionableSourceNotFoundException)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>
+<DD>If the optionable load file can not be found this error is signalled.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleSaveException(java.lang.Exception)"><B>handleSaveException(Exception)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleSaveException(java.lang.Exception)"><B>handleSaveException(Exception)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>
+<DD>If something nasty occurs whilst gather the optionable
+ information occurs this is error is signalled.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleSaveException(java.io.IOException)"><B>handleSaveException(IOException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleSaveException(java.io.IOException)"><B>handleSaveException(IOException)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>
+<DD>If the save encounters IO problems!
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>HardModificationSetFactory</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>.<DD>HardModificationSetFactory.java
+
+
+ Created: Wed Mar 1 15:04:37 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#HardModificationSetFactory()"><B>HardModificationSetFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#hash"><B>hash</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html">InvokerThreadManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#hashCode()"><B>hashCode()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#hashCode()"><B>hashCode()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#hasListeners()"><B>hasListeners()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#hasListeners()"><B>hasListeners()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>There is really no point in making an event object if there are
+ no listeners.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#hasListeners(java.lang.String)"><B>hasListeners(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#hasListeners(java.lang.String)"><B>hasListeners(String)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#hasNext()"><B>hasNext()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#HISTIDINE"><B>HISTIDINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_I_"><!-- --></A><H2>
+<B>I</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A> - interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>.<DD>Identifiable.java
+
+
+ Created: Wed Jul 5 16:04:31 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>Identifier</B></A> - interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>.<DD>SequenceIdentifier.java
+
+
+ Created: Mon Jul 3 16:07:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#identifierStart(org.xml.sax.Attributes)"><B>identifierStart(Attributes)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#ignorableWhitespace(char[], int, int)"><B>ignorableWhitespace(char[], int, int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html"><B>IllegalDuplicateModificationException</B></A> - exception uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html">IllegalDuplicateModificationException</A>.<DD>IllegalDuplicateModificationException.java
+
+
+ Created: Mon Feb 28 23:57:13 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html#IllegalDuplicateModificationException(java.lang.String)"><B>IllegalDuplicateModificationException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html">IllegalDuplicateModificationException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#indexOf(int)"><B>indexOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#indexOf(uk.ac.man.bioinf.module.Module)"><B>indexOf(Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Returns the index of a module.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#indexOf(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>indexOf(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Returns the index of a module identifier.
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#indexOf(java.lang.Object)"><B>indexOf(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#indexOf(java.lang.Object, int)"><B>indexOf(Object, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>IndividualElementColorMap</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html">IndividualElementColorMap</A>.<DD>IndividualElementColorMap.java
+
+ Allows a direct mapping between an element and a color; thereby
+ every element in a sequence type will have an associated color.<DT><A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html#IndividualElementColorMap(java.lang.String, uk.ac.man.bioinf.sequence.Element[], java.awt.Color[])"><B>IndividualElementColorMap(String, Element[], Color[])</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html">IndividualElementColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#init()"><B>init()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#init(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[], uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>init(GappedSequence[], SequenceType, int[], Identifier)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#INSERT"><B>INSERT</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>
+<DD>Event type indicating a new sequence has been added to the
+ sequence alignment
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html#INSERT"><B>INSERT</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>
+<DD>Indicates a insertion event
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><B>insertElementAt(Element[], int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>
+<DD>Inserts the elements at this position.
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><B>insertElementAt(Element[], int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>Provides a trivial implementation of this method by calling
+ multiple single insert methods.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element, int)"><B>insertElementAt(Element, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>
+<DD>Insert the element at the specified index.
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element, int)"><B>insertElementAt(Element, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#insertElementAt(java.lang.Object, int)"><B>insertElementAt(Object, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><B>insertElementAtQuietly(Element, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><B>insertElementAtQuietly(Element, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int)"><B>insertGapAt(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#insertGapAt(int)"><B>insertGapAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAt(int)"><B>insertGapAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#insertGapAt(int)"><B>insertGapAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int, int)"><B>insertGapAt(int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>
+<DD>Inserts the elements at this position.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#insertGapAt(int, int)"><B>insertGapAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAt(int, int)"><B>insertGapAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#insertGapAt(int, int)"><B>insertGapAt(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#insertGapAtQuietly(int)"><B>insertGapAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#insertGapAtQuietly(int)"><B>insertGapAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAtQuietly(int)"><B>insertGapAtQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#insertGapsAt(int, int, int)"><B>insertGapsAt(int, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#insertGapsAt(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int)"><B>insertGapsAt(SequenceAlignmentPoint, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#insertGapsAtCursor(int)"><B>insertGapsAtCursor(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)"><B>insertString(int, String, AttributeSet)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html">WholeNumberField.WholeNumberDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)"><B>insertString(int, String, AttributeSet)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html">IntegerField.IntegerDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)"><B>insertString(int, String, AttributeSet)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html">FormattedDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#INSET_CHANGE"><B>INSET_CHANGE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>
+<DD>Event type indicating a change in the inset/preceeding number of gaps
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/Install.html"><B>Install</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html">Install</A>.<DD>Install.java
+
+ This class provides the install information for the all of the
+ classes in the viewer package.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/Install.html#Install()"><B>Install()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html">Install</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#installAlignmentListeners(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>installAlignmentListeners(ConsensusCalculator)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/Install.html#installBasicLookAndFeel()"><B>installBasicLookAndFeel()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html">Install</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#installKeyboardActions(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>installKeyboardActions(JAlignmentViewer)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#installListeners()"><B>installListeners()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#installUI(javax.swing.JComponent)"><B>installUI(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#installVetoListeners()"><B>installVetoListeners()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html#instance"><B>instance</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html#instance"><B>instance</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html#instance"><B>instance</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#INSTANCE"><B>INSTANCE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>InstancePerAlignmentColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html">InstancePerAlignmentColorMapMetaData</A>.<DD>InstancePerAlignmentColorMapMetaData.java
+
+
+ Created: Wed Jul 19 14:50:50 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#InstancePerAlignmentColorMapMetaData()"><B>InstancePerAlignmentColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html">InstancePerAlignmentColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html"><B>IntArrayList</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>.<DD>IntArrayList.java
+
+ This class provides something akin to the ArrayList class but with
+ all the methods typed as ints, which avoids the additional bloat of
+ having to create an object for every containined integer.<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#IntArrayList()"><B>IntArrayList()</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#IntArrayList(int)"><B>IntArrayList(int)</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>IntegerField</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>IntegerField.IntegerDocument</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html">IntegerField.IntegerDocument</A>.<DD>&nbs [...]
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html">IntegerField.IntegerDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html#IntegerField(int)"><B>IntegerField(int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html#IntegerField(int, int)"><B>IntegerField(int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>IntenseColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#IntenseColorMapMetaData()"><B>IntenseColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html"><B>InvalidSequenceTypeException</B></A> - exception uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A>.<DD>InvalidSequenceTypeException.java
+
+ Exception to signal that an attempt has been made to use a sequence
+ of an invalid type.<DT><A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html#InvalidSequenceTypeException(java.lang.String)"><B>InvalidSequenceTypeException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html"><B>InvalidSequenceTypeParserException</B></A> - exception uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>.<DD>This exception is cast when there is a mismatch of sequence types
+ when dealing with parsers.<DT><A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException()"><B>InvalidSequenceTypeParserException()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException(uk.ac.man.bioinf.sequence.SequenceType)"><B>InvalidSequenceTypeParserException(SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException(java.lang.String)"><B>InvalidSequenceTypeParserException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException(java.lang.String, uk.ac.man.bioinf.sequence.SequenceType)"><B>InvalidSequenceTypeParserException(String, SequenceType)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>InvertedScrollPaneLayout</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html">InvertedScrollPaneLayout</A>.<DD>InvertedScrollPaneLayout.java
+
+
+ Created: Fri Mar 31 14:27:41 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html#InvertedScrollPaneLayout()"><B>InvertedScrollPaneLayout()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html">InvertedScrollPaneLayout</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>Invoker</B></A> - class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>.<DD>Invoker.java
+
+ This class another attempt at making the sytem event queue easier
+ in Swing.<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#Invoker()"><B>Invoker()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>Pointless constructor provided for the hell of it.
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#Invoker(java.lang.Object)"><B>Invoker(Object)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>Less Pointless constructor.
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#Invoker(java.lang.Object, java.lang.Object)"><B>Invoker(Object, Object)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>Even more less pointless contstructor
+ Takes a param to be used later as a parameter
+ for the method which will be called on what is proably
+ going to be the source.
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html"><B>InvokerInternalEventQueueException</B></A> - exception uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html">InvokerInternalEventQueueException</A>.<DD>InvokerInternalEventQueueException.java
+
+ For translating a generic exception into a runtime exception
+
+ Created: Fri Oct 01 15:18:01 1999<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html#InvokerInternalEventQueueException(java.lang.Exception)"><B>InvokerInternalEventQueueException(Exception)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html">InvokerInternalEventQueueException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>InvokerInternalQueue</B></A> - class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>.<DD>InvokerInternalQueue.java
+
+ This class is used as a helper mechanism for interacting with swing
+ objects.<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#InvokerInternalQueue()"><B>InvokerInternalQueue()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#InvokerInternalQueue(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer)"><B>InvokerInternalQueue(SystemEventProducer)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#InvokerInternalQueue(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, java.util.List)"><B>InvokerInternalQueue(SystemEventProducer, List)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>A new queue.
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html"><B>InvokerInternalQueueException</B></A> - exception uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html">InvokerInternalQueueException</A>.<DD>InvokerInternalQueueException.java
+
+
+ Created: Fri Dec 1 17:57:48 2000<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html#InvokerInternalQueueException(java.lang.String)"><B>InvokerInternalQueueException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html">InvokerInternalQueueException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html"><B>InvokerThreadManager</B></A> - class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html">InvokerThreadManager</A>.<DD>InvokerThreadManager.java
+
+
+ Created: Tue Nov 7 18:47:34 2000<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#InvokerThreadManager()"><B>InvokerThreadManager()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html">InvokerThreadManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><B>isAllowableElement(ComplexElement)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><B>isAllowableElement(ComplexElement)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>
+<DD>Is this given element allowable in this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><B>isAllowableElement(ComplexElement)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#isAnchored(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><B>isAnchored(CinemaGroup)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#isCurrentlySelected()"><B>isCurrentlySelected()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#isDecimalFieldValid(java.lang.String)"><B>isDecimalFieldValid(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#isDestroyed()"><B>isDestroyed()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#isDestroyed()"><B>isDestroyed()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char)"><B>isElement(char)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(char)"><B>isElement(char)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)"><B>isElement(char)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(char)"><B>isElement(char)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char[])"><B>isElement(char[])</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(char[])"><B>isElement(char[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])"><B>isElement(char[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(char[])"><B>isElement(char[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)"><B>isElement(Element)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)"><B>isElement(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)"><B>isElement(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)"><B>isElement(Element)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])"><B>isElement(Element[])</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])"><B>isElement(Element[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])"><B>isElement(Element[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])"><B>isElement(Element[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#isEmpty()"><B>isEmpty()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#isEmpty()"><B>isEmpty()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Returns whether the list is empty.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#isEmpty()"><B>isEmpty()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Returns whether the list is empty.
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#isEmpty()"><B>isEmpty()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#isEnd(int)"><B>isEnd(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html">SequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#isEnd(int)"><B>isEnd(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#isIntegerFieldValid(java.lang.String)"><B>isIntegerFieldValid(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html#isInterface()"><B>isInterface()</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>
+<DD>Returns whether this module is an interface.
+<DT><A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html#isInterface()"><B>isInterface()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/GenericModuleIdentifier.html">GenericModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#isInterface()"><B>isInterface()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)"><B>isModification(Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)"><B>isModification(Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>
+<DD>Is this modification one which is allowable in this sequence
+ type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)"><B>isModification(Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])"><B>isModification(Modification[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])"><B>isModification(Modification[])</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>
+<DD>Are these modifications allowable in this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])"><B>isModification(Modification[])</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#isModified(uk.ac.man.bioinf.sequence.complex.Modification)"><B>isModified(Modification)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html#isModified(uk.ac.man.bioinf.sequence.complex.Modification)"><B>isModified(Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>isModuleAvailable(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>isModuleAvailable(ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Returns whether a module is available for use.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>isModuleAvailable(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>Returns whether a module is available for use, given the
+ identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>isModuleAvailable(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#isModuleIdentifier()"><B>isModuleIdentifier()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#ISOLEUCINE"><B>ISOLEUCINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#isPasswordToBeRemembered()"><B>isPasswordToBeRemembered()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>isPointSelected(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>isPointSelected(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>isPointSelected(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>isPointSelected(SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Is the point within one of the selection rectangles
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#isReadonly()"><B>isReadonly()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#isSelecting()"><B>isSelecting()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#isSelecting()"><B>isSelecting()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#isSelecting()"><B>isSelecting()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isSelecting()"><B>isSelecting()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>is the current selection in the process of being selected.
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#isStarted()"><B>isStarted()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>Returns whether the module has been started (ie: the start method
+ run).
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#isTextFieldValid(java.lang.String)"><B>isTextFieldValid(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html#isValid()"><B>isValid()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html#isValid()"><B>isValid()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">DecimalField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#isValueAdjusting()"><B>isValueAdjusting()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html#itemStateChanged(java.awt.event.ItemEvent)"><B>itemStateChanged(ItemEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html">ButtonViewerPopupMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html#itemStateChanged(java.awt.event.ItemEvent)"><B>itemStateChanged(ItemEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html">ButtonPanelTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#iterator()"><B>iterator()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Returns an iterator of all the sequences.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#iterator()"><B>iterator()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#iterator()"><B>iterator()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)"><B>iterator(Class)</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_J_"><!-- --></A><H2>
+<B>J</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>JAlignmentButtonPanel</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>.<DD>JAlignmentButtonPanel.java
+
+ This component provides a rank of Buttons relating to a
+ SequenceAlignment.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#JAlignmentButtonPanel()"><B>JAlignmentButtonPanel()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#JAlignmentButtonPanel(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>JAlignmentButtonPanel(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>JAlignmentRuler</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>.<DD>JAlignmentRuler.java
+
+
+
+ Created: Thu Mar 23 12:33:50 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler()"><B>JAlignmentRuler()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>JAlignmentRuler(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)"><B>JAlignmentRuler(SequenceAlignment, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int, int)"><B>JAlignmentRuler(SequenceAlignment, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>JAlignmentViewer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>.<DD>JAlignmentViewer.java
+
+
+ Created: Tue Mar 14 16:28:59 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#JAlignmentViewer()"><B>JAlignmentViewer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#JAlignmentViewer(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>JAlignmentViewer(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>JChangedScrollPane</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html">JChangedScrollPane</A>.<DD>JChangedScrollPane.java
+
+
+ Created: Fri Mar 31 14:56:45 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html#JChangedScrollPane(java.awt.Component, int, int)"><B>JChangedScrollPane(Component, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html">JChangedScrollPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html#JChangedScrollPane(javax.swing.ScrollPaneLayout, java.awt.Component, int, int)"><B>JChangedScrollPane(ScrollPaneLayout, Component, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html">JChangedScrollPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>JLayableScrollPane</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html">JLayableScrollPane</A>.<DD>JLayableScrollPane.java
+
+ You cant reset the layout manager on a scroll pane, due to what
+ appears to be a bug in the JScrollPane layout, at least not it you
+ want anything to appear on screen.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html#JLayableScrollPane(java.awt.Component, int, int)"><B>JLayableScrollPane(Component, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html">JLayableScrollPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html#JLayableScrollPane(javax.swing.ScrollPaneLayout, java.awt.Component, int, int)"><B>JLayableScrollPane(ScrollPaneLayout, Component, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html">JLayableScrollPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>Js_TestColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#Js_TestColorMapMetaData()"><B>Js_TestColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_K_"><!-- --></A><H2>
+<B>K</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#killSplash()"><B>killSplash()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html">CinemaSplash</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_L_"><!-- --></A><H2>
+<B>L</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#lastElement()"><B>lastElement()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#lastIndexOf(int)"><B>lastIndexOf(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#lastIndexOf(java.lang.Object)"><B>lastIndexOf(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#lastIndexOf(java.lang.Object, int)"><B>lastIndexOf(Object, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html#layoutContainer(java.awt.Container)"><B>layoutContainer(Container)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html">InvertedScrollPaneLayout</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#LEFT"><B>LEFT</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#LENGTH_CHANGE"><B>LENGTH_CHANGE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>
+<DD>Event type indicating that the length of the alignment has
+ changed.
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorList.html#length()"><B>length()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#LESS_THAN"><B>LESS_THAN</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#LEUCINE"><B>LEUCINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#LIKE"><B>LIKE</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#linearSearch(int)"><B>linearSearch(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>Provides a linear search.
+<DT><A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html#linearSearch(java.lang.Object[], java.lang.Object)"><B>linearSearch(Object[], Object)</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html">ArrayManipulation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html">CinemaSplash</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#load()"><B>load()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>The method called for the load of this module.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>load(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html">CinemaModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>load(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>load(ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Loads the module associated with a particular identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>load(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#loadEnd()"><B>loadEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#loadOptions()"><B>loadOptions()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#LYSINE"><B>LYSINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_M_"><!-- --></A><H2>
+<B>M</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html">Cinema</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html">CinemaTestModuleLaunch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html">CinemaTestLaunch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html">CinemaResizeElements</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html">SequenceSearch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html">GappedSequenceSearch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html">CalculatePercentageID</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html">XMLStartTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html">SliderExample</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html">SingleSelectionModelTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html">ButtonPanelTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html">AlignmentViewerTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.io.test.<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html">AlignmentParserInputTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.io.test.<A HREF="uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html">AlignmentParserIOTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html">SequencesTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html">SequenceFactoryTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html">SequenceColumnTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html">GappedSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html">GappableSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html">EditableSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html">ComplexSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html">ComplexElementAndModificationTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html#main(java.lang.String[])"><B>main(String[])</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html">ArrayManipulation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#makeEmpty()"><B>makeEmpty()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html"><B>MalformedAccessionException</B></A> - exception uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html">MalformedAccessionException</A>.<DD>MalformedAccessionException.java
+
+ Used to indicate an inappropriate accession number has been
+ entered.<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html#MalformedAccessionException(java.lang.String)"><B>MalformedAccessionException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html">MalformedAccessionException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html#mark(int)"><B>mark(int)</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html">NarrowedInputStream</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Class, java.lang.Object)"><B>message(Class, Object)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.Object)"><B>message(Class, Object)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Class, java.lang.Object)"><B>message(Class, Object)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.Object)"><B>message(Class, Object)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/NullDebug.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/NullDebug.html">NullDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html">DefaultFileDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html">DefaultDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)"><B>message(Class, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Object, java.lang.Object)"><B>message(Object, Object)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.Object)"><B>message(Object, Object)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Object, java.lang.Object)"><B>message(Object, Object)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Object, java.lang.Object)"><B>message(Object, Object)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Object, java.lang.String)"><B>message(Object, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.String)"><B>message(Object, String)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Object, java.lang.String)"><B>message(Object, String)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Object, java.lang.String)"><B>message(Object, String)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html"><B>MetalAlignmentViewerUI</B></A> - class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html">MetalAlignmentViewerUI</A>.<DD>MetalAlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:32:29 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html#MetalAlignmentViewerUI()"><B>MetalAlignmentViewerUI()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html">MetalAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#METHIONINE"><B>METHIONINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>Methylation</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html">Methylation</A>.<DD>Methylation.java
+
+
+ Created: Tue Feb 29 11:44:59 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html#METHYLATION"><B>METHYLATION</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html">Methylation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html"><B>Modification</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>.<DD>Modification.java
+
+
+ Created: Mon Feb 28 20:42:16 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>ModificationFactory</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html">ModificationFactory</A>.<DD>ModificationFactory.java
+
+
+ Created: Mon Feb 28 23:07:50 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html#ModificationFactory()"><B>ModificationFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html">ModificationFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html"><B>ModificationSetFactoryInterface</B></A> - interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>.<DD>ModificationSetFactoryInterface.java
+
+
+ Created: Wed Mar 1 15:01:48 2000<DT><A HREF="uk/ac/man/bioinf/module/Module.html"><B>Module</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>.<DD>Module.java
+
+ Represents a module, the main constituent of a modular
+ architectured program.<DT><A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_CLASS_NOT_FOUND"><B>MODULE_CLASS_NOT_FOUND</B></A> -
+Static variable in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A>
+<DD>The module class was not found in the location stated.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_DOES_NOT_EXIST"><B>MODULE_DOES_NOT_EXIST</B></A> -
+Static variable in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_EXISTS"><B>MODULE_EXISTS</B></A> -
+Static variable in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A>
+<DD>The module has previously been defined and created.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_INIT_PROBLEM"><B>MODULE_INIT_PROBLEM</B></A> -
+Static variable in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A>
+<DD>Creating and instantiating the module generated a problem.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_RESOLVE_FAIL"><B>MODULE_RESOLVE_FAIL</B></A> -
+Static variable in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A>
+<DD>Indicates a failed attempt to resolve a module name
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#Module()"><B>Module()</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html"><B>ModuleContext</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>.<DD>ModuleContext.java
+
+ Gives context to a module (e.g: configuration information).<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#ModuleContext()"><B>ModuleContext()</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#moduleEnd()"><B>moduleEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html"><B>ModuleException</B></A> - exception uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>.<DD>ModuleException.java
+
+ An exception thrown if a module does not load sucessfully.<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#ModuleException(uk.ac.man.bioinf.module.ModuleExceptionType)"><B>ModuleException(ModuleExceptionType)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.String)"><B>ModuleException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.String, uk.ac.man.bioinf.module.ModuleExceptionType)"><B>ModuleException(String, ModuleExceptionType)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.String, uk.ac.man.bioinf.module.ModuleExceptionType, java.lang.Throwable)"><B>ModuleException(String, ModuleExceptionType, Throwable)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.Throwable)"><B>ModuleException(Throwable)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>ModuleExceptionType</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A>.<DD>This class provides an identifier for the module exception that has
+ been thrown, rather than string comparisons needing to be carried
+ out.<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html"><B>ModuleFactoryInstance</B></A> - interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>.<DD>ModuleFactoryInstance.java
+
+ This interface is designed to provide a means of storing loaded
+ modules and their associated identifiers.<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html"><B>ModuleIdentifier</B></A> - interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>.<DD>ModuleIdentifier.java
+
+ A thin tag for a module, rather than banding round modules.<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>ModuleIdentifierList</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>.<DD>To provide a list of module identifiers in a type safe manor.<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#ModuleIdentifierList(java.util.List)"><B>ModuleIdentifierList(List)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html"><B>ModuleList</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>.<DD>To provide a list of modules in a type safe manor.<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#ModuleList(java.util.List)"><B>ModuleList(List)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>ModuleStorageStructure</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>.<DD>ModuleStorageStructure.java
+
+ Stores the module (if it exists), the context, the module
+ configuration object and the required modules for one module
+ identifier.<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#ModuleStorageStructure()"><B>ModuleStorageStructure()</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#ModuleStorageStructure(uk.ac.man.bioinf.module.ModuleContext)"><B>ModuleStorageStructure(ModuleContext)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#ModuleStorageStructure(uk.ac.man.bioinf.module.ModuleContext, java.lang.Object)"><B>ModuleStorageStructure(ModuleContext, Object)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html"><B>MotProteinParser</B></A> - class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html">MotProteinParser</A>.<DD>MotProteinParser.java
+
+ Mot files are used by several of the applications that are used to
+ produce PRINTS.<DT><A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html#MotProteinParser()"><B>MotProteinParser()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html">MotProteinParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseClicked(java.awt.event.MouseEvent)"><B>mouseClicked(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#mouseDragged(java.awt.event.MouseEvent)"><B>mouseDragged(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html">SwappingListBasicUI.SwappingMouseInputHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseDragged(java.awt.event.MouseEvent)"><B>mouseDragged(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseEntered(java.awt.event.MouseEvent)"><B>mouseEntered(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseExited(java.awt.event.MouseEvent)"><B>mouseExited(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseMoved(java.awt.event.MouseEvent)"><B>mouseMoved(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#mousePressed(java.awt.event.MouseEvent)"><B>mousePressed(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html">SwappingListBasicUI.SwappingMouseInputHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mousePressed(java.awt.event.MouseEvent)"><B>mousePressed(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseReleased(java.awt.event.MouseEvent)"><B>mouseReleased(MouseEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#move(int, int)"><B>move(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Allows the moving of a point to a new position.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursor(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>moveCursor(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorBeginningOfAlignment()"><B>moveCursorBeginningOfAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorBeginningOfSequence()"><B>moveCursorBeginningOfSequence()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorDown(int)"><B>moveCursorDown(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorEndOfAlignment()"><B>moveCursorEndOfAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorEndOfSequence()"><B>moveCursorEndOfSequence()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorLeft(int)"><B>moveCursorLeft(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageDown()"><B>moveCursorPageDown()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageLeft()"><B>moveCursorPageLeft()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageRight()"><B>moveCursorPageRight()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageUp()"><B>moveCursorPageUp()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorRight(int)"><B>moveCursorRight(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorToSequencePoint(int, int)"><B>moveCursorToSequencePoint(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorToSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>moveCursorToSequencePoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorUp(int)"><B>moveCursorUp(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>MultiplexerFastAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A>.<DD>MultiplexerFastAlignmentViewerCellRenderer.java
+
+ This multiplexer uses three other cell renderers to render the cell.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#MultiplexerFastAlignmentViewerCellRenderer(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>MultiplexerFastAlignmentViewerCellRenderer(JAlignmentViewer)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>.<DD>MutableSequence.java
+
+ A marker class to present a sequence which can be changed without
+ the necessity for generating a new sequence.</DL>
+<HR>
+<A NAME="_N_"><!-- --></A><H2>
+<B>N</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#NAME"><B>NAME</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html"><B>NamedAlignmentSelectionModel</B></A> - class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>.<DD>NamedAlignmentSelectionModel.java
+
+ Stores multiple selections each one with a name.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#NamedAlignmentSelectionModel()"><B>NamedAlignmentSelectionModel()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#nameEnd()"><B>nameEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>NarrowedInputStream</B></A> - class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html">NarrowedInputStream</A>.<DD>NarrowedInputStream.java
+
+ This InputStream wraps another and puts a limits access to that
+ stream.<DT><A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html#NarrowedInputStream(java.io.InputStream, byte[], byte[])"><B>NarrowedInputStream(InputStream, byte[], byte[])</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html">NarrowedInputStream</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html#next()"><B>next()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#next()"><B>next()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html#NO_VETO"><B>NO_VETO</B></A> -
+Static variable in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>
+<DD>This value should be used when the system is going to
+ shutdown regardless of errors
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#nodeEnd()"><B>nodeEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#nodeStart()"><B>nodeStart()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html"><B>NoGapAtThisPositionException</B></A> - exception uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>.<DD>NoGapAtThisPositionException.java
+
+
+ Created: Sat Mar 4 14:04:07 2000<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#NoGapAtThisPositionException(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>NoGapAtThisPositionException(GappedSequence, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#NoGapAtThisPositionException(java.lang.String)"><B>NoGapAtThisPositionException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#NoGapAtThisPositionException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><B>NoGapAtThisPositionException(String, GappedSequence, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>
+<DD>Creates an object signalling an exception for no gap at a
+ particular position.
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>NoIdentifier</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A>.<DD>NoSequenceIdentifier.java
+
+
+ Created: Wed Jul 5 18:42:11 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#NoIdentifier()"><B>NoIdentifier()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#NoIdentifier(uk.ac.man.bioinf.sequence.identifier.Source)"><B>NoIdentifier(Source)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/Direction.html#NORTH"><B>NORTH</B></A> -
+Static variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Direction.html">Direction</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>NoSource</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html">NoSource</A>.<DD>NoSource.java
+
+
+ Created: Wed Jul 5 18:11:08 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html#NoSource()"><B>NoSource()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html">NoSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html"><B>NoSuchModificationException</B></A> - exception uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html">NoSuchModificationException</A>.<DD>NoSuchModificationException.java
+
+
+ Created: Tue Feb 29 00:09:26 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html#NoSuchModificationException(java.lang.String)"><B>NoSuchModificationException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html">NoSuchModificationException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html"><B>NoSuchRequiredModule</B></A> - exception uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html">NoSuchRequiredModule</A>.<DD>NoSuchRequiredModule.java
+
+
+ Created: Mon Nov 13 15:24:02 2000<DT><A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html#NoSuchRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>NoSuchRequiredModule(ModuleIdentifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html">NoSuchRequiredModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html"><B>NoSuchSequenceElementException</B></A> - exception uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>.<DD>NoSuchSequenceElementException.java
+
+
+ Created: Fri Mar 3 12:22:15 2000<DT><A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException()"><B>NoSuchSequenceElementException()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException(uk.ac.man.bioinf.sequence.Sequence, int)"><B>NoSuchSequenceElementException(Sequence, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException(java.lang.String)"><B>NoSuchSequenceElementException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException(java.lang.String, uk.ac.man.bioinf.sequence.Sequence, int)"><B>NoSuchSequenceElementException(String, Sequence, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html"><B>NoSuchSequenceException</B></A> - exception uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A>.<DD>NoSuchSequenceException.java
+
+ Alerts to an invalid sequence index within a sequence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException()"><B>NoSuchSequenceException()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)"><B>NoSuchSequenceException(SequenceAlignment, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException(java.lang.String)"><B>NoSuchSequenceException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)"><B>NoSuchSequenceException(String, SequenceAlignment, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>NucleotideResidue</B></A> - interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>.<DD>NucleotideResidue.java
+
+ An interface to mark up nucleotide residues.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>NullAlignmentSelectionModel</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>.<DD>NullAlignmentSelectionModel.java
+
+ Trivial selection model.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>NullColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html">NullColorMapMetaData</A>.<DD>NullColorMapMetaData.java
+
+
+ Created: Fri Jul 21 15:57:31 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#NullColorMapMetaData()"><B>NullColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html">NullColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/NullDebug.html"><B>NullDebug</B></A> - class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/NullDebug.html">NullDebug</A>.<DD>NullDebug.java
+
+ This class does nothing with debug methods.<DT><A HREF="uk/ac/man/bioinf/debug/NullDebug.html#NullDebug()"><B>NullDebug()</B></A> -
+Constructor for class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/NullDebug.html">NullDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html"><B>NullModuleFactory</B></A> - class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>.<DD>NullModuleFactory.java
+
+ This class does precisely nothing, but in a very special way.....<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#NullModuleFactory()"><B>NullModuleFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>NullOptionHandler</B></A> - class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html">NullOptionHandler</A>.<DD>NullOptionHandler.java
+
+ An option handler object that does nothing.<DT><A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html"><B>NullParserExceptionHandler</B></A> - class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html">NullParserExceptionHandler</A>.<DD>NullParserExceptionHandler.java
+
+ An exception handler for all seasons
+
+ Created: Thu Feb 8 21:24:57 2001<DT><A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html#NullParserExceptionHandler()"><B>NullParserExceptionHandler()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html">NullParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html#NullParserExceptionHandler(boolean)"><B>NullParserExceptionHandler(boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html">NullParserExceptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html#NullParserExceptionHandler(java.io.PrintWriter)"><B>NullParserExceptionHandler(PrintWriter)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html">NullParserExceptionHandler</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_O_"><!-- --></A><H2>
+<B>O</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#openAlignment()"><B>openAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#openAlignment()"><B>openAlignment()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>Obtains the sequence alignment by the relevent method.
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#openFile(java.io.File)"><B>openFile(File)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#openFile(java.io.File, uk.ac.man.bioinf.io.AlignmentInputParser, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>openFile(File, AlignmentInputParser, Identifier)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A>
+<DD>Opens a file using a parser.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#openFile(java.lang.String, java.lang.String)"><B>openFile(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>
+<DD>Opens a declared file in Cinema.
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html"><B>Optionable</B></A> - interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>.<DD>Optionable.java
+
+ An object implementing this interface may be in several
+ different states, that is provide options.<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html"><B>OptionableExceptionHandler</B></A> - interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>.<DD>OptionableExceptionHandler.java
+
+
+ Created: Mon May 14 14:04:22 2001<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>OptionableJFrame</B></A> - class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>.<DD>OptionableJFrame.java
+
+
+ Created: Fri May 07 16:45:36 1999<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String)"><B>OptionableJFrame(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, boolean)"><B>OptionableJFrame(String, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>No title.
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, java.lang.String)"><B>OptionableJFrame(String, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>An internal frame with a title
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, java.lang.String, boolean)"><B>OptionableJFrame(String, String, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, java.lang.String, boolean, uk.ac.man.bioinf.apps.optionable.OptionHandler)"><B>OptionableJFrame(String, String, boolean, OptionHandler)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>A title and the ability to delay the registering of the optionable
+ status
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html"><B>OptionableJSplitPane</B></A> - class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>.<DD>OptionableJSplitPane.java
+
+ Stores the divider location as an option
+
+ Created: Fri Feb 2 17:55:18 2001<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#OptionableJSplitPane(java.lang.String)"><B>OptionableJSplitPane(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#OptionableJSplitPane(java.lang.String, int)"><B>OptionableJSplitPane(String, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html"><B>OptionableSourceNotFoundException</B></A> - exception uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A>.<DD>OptionableSourceNotFoundException.java
+
+
+ Created: Mon May 14 14:13:40 2001<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html#OptionableSourceNotFoundException()"><B>OptionableSourceNotFoundException()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html#OptionableSourceNotFoundException(java.lang.String)"><B>OptionableSourceNotFoundException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html"><B>OptionableStateException</B></A> - exception uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">OptionableStateException</A>.<DD>OptionableStateException.java
+
+ This exception is thrown when an Optionable object is in an illegal
+ state.<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html#OptionableStateException(java.lang.String)"><B>OptionableStateException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">OptionableStateException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html"><B>OptionHandler</B></A> - interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>.<DD>OptionHandler.java
+
+ Objects implementing this interface should record all of
+ Optionable object, storing and restoring their options
+ as necessary
+
+ Created: Mon Feb 01 18:10:52 1999<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html#ord"><B>ord</B></A> -
+Variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_P_"><!-- --></A><H2>
+<B>P</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>PackageResourceAdapter</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A>.<DD>Looks specifically for resources in the package 'resource' that should be at the route of the Application's class path.<DT><A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html#PackageResourceAdapter(java.lang.String)"><B>PackageResourceAdapter(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paint(java.awt.Graphics, javax.swing.JComponent)"><B>paint(Graphics, JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#paint(java.awt.Graphics, javax.swing.JComponent)"><B>paint(Graphics, JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintCells(java.awt.Graphics, javax.swing.JComponent)"><B>paintCells(Graphics, JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html#paintComponent(java.awt.Graphics, java.awt.Component, java.awt.Container, int, int, int, int, boolean)"><B>paintComponent(Graphics, Component, Container, int, int, int, int, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html">CellRendererPaneReplacement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintFocusRect(java.awt.Graphics, java.awt.Rectangle)"><B>paintFocusRect(Graphics, Rectangle)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintImmediately(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>paintImmediately(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintSelection(java.awt.Graphics, javax.swing.JComponent)"><B>paintSelection(Graphics, JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#paintThumb(java.awt.Graphics)"><B>paintThumb(Graphics)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#paintTrack(java.awt.Graphics)"><B>paintTrack(Graphics)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#paramEnd()"><B>paramEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#paramnameEnd()"><B>paramnameEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#parent"><B>parent</B></A> -
+Variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Identifier, Reader, ParserExceptionHandler)</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Identifier, Reader, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Identifier, Reader, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html">FastaSequenceParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Reader, ParserExceptionHandler)</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Reader, ParserExceptionHandler)</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>
+<DD>This method returns a sequence alignment from a buffered reader
+ input stream.
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Reader, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A>
+<DD>This function parses an input reader which contains a (set of)
+ PIR/NBRF sequence(s), and returns an alignment containing
+ them.
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>parse(Reader, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html">FastaSequenceParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#parseResource(java.lang.String, boolean)"><B>parseResource(String, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html"><B>ParserException</B></A> - exception uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>.<DD>A general exception thrown up when parsing a sequence.<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#ParserException(int)"><B>ParserException(int)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#ParserException(int, java.lang.String)"><B>ParserException(int, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#ParserException(java.lang.String, int)"><B>ParserException(String, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#ParserException(java.lang.String, int, java.lang.String)"><B>ParserException(String, int, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserException.html#ParserException(java.lang.String, int, java.lang.String, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>ParserException(String, int, String, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserException.html">ParserException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html"><B>ParserExceptionHandler</B></A> - interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>.<DD>Handles exceptions generated by any sequence parsers.<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#parseStream(java.io.InputStream)"><B>parseStream(InputStream)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#password"><B>password</B></A> -
+Variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>PasswordDialog</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>.<DD>Pop up Dialog box to get a password off a user.<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame)"><B>PasswordDialog(JFrame)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String)"><B>PasswordDialog(JFrame, String, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String, java.lang.String, java.lang.String)"><B>PasswordDialog(JFrame, String, String, String, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean)"><B>PasswordDialog(JFrame, String, String, String, String, String, boolean)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>PedanticColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#PedanticColorMapMetaData()"><B>PedanticColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#peek()"><B>peek()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html"><B>PercentageIDCalculator</B></A> - class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>.<DD>PercentageIDCalculator.java
+
+ This class performs a variance calculation on the given sequence
+ alignment.<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#PercentageIDCalculator(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>PercentageIDCalculator(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html"><B>PercentageIDCalculatorManager</B></A> - class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A>.<DD>PercentageIDCalculatorManager.java
+
+
+ Created: Tue Nov 7 17:59:02 2000<DT><A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html#PercentageIDCalculatorManager()"><B>PercentageIDCalculatorManager()</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>PercentageIDConsensus</B></A> - class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A>.<DD>PercentageIDConsensus.java
+
+ Calculates a consensus sequence based simply on which element is
+ most frequent at that row.<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#PercentageIDConsensus(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator)"><B>PercentageIDConsensus(PercentageIDCalculator)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>PercentageIDConsensusCalculatorMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>.<DD>PercentageIDConsensusCalculatorMetaData.java
+
+
+ Created: Thu Jul 27 16:46:59 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#PercentageIDConsensusCalculatorMetaData()"><B>PercentageIDConsensusCalculatorMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>PercentageIDVarianceColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A>.<DD>PercentageIDVarianceColorMapMetaData.java
+
+
+ Created: Wed Jul 19 15:00:44 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#PercentageIDVarianceColorMapMetaData()"><B>PercentageIDVarianceColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>PercentIDVarianceColorMap</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>.<DD>PercentIDVarianceColorMap.java
+
+ Calculates a colour scheme
+
+ Created: Fri Jun 9 16:03:46 2000<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#PercentIDVarianceColorMap(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator)"><B>PercentIDVarianceColorMap(PercentageIDCalculator)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#PercentIDVarianceColorMap(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator, uk.ac.man.bioinf.gui.color.ColorList)"><B>PercentIDVarianceColorMap(PercentageIDCalculator, ColorList)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#PHENYLALANINE"><B>PHENYLALANINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html"><B>PIRProteinAlignmentParser</B></A> - class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A>.<DD>A filter that reads an alignment in PIR/NBRF protein sequence
+ format and returns a sequence alignment object.<DT><A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#PIRProteinAlignmentParser()"><B>PIRProteinAlignmentParser()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#pop()"><B>pop()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>PopUpHtmlDisplay</B></A> - class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html">PopUpHtmlDisplay</A>.<DD>Displays an URL with a single 'OK' button at the bottom<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#preferredHeight"><B>preferredHeight</B></A> -
+Variable in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#print()"><B>print()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#print(java.awt.Graphics, java.awt.print.PageFormat, int)"><B>print(Graphics, PageFormat, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html#print(java.util.Map)"><B>print(Map)</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html">CollectionPrinter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html#print(java.lang.Object[])"><B>print(Object[])</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html">CollectionPrinter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>PrintableAlignmentPanel</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html">PrintableAlignmentPanel</A>.<DD>PrintableAlignmentPanel.java
+
+
+ Created: Fri Mar 9 20:00:24 2001<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html#PrintableAlignmentPanel()"><B>PrintableAlignmentPanel()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html">PrintableAlignmentPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>PrintableJAlignmentViewer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>.<DD>PrintableJAlignmentViewer.java
+
+ A JAlignmentViewer which can be used to print
+
+ Created: Fri Mar 9 17:21:44 2001<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#PrintableJAlignmentViewer(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>PrintableJAlignmentViewer(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#printAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>printAlignment(SequenceAlignment)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#printElements(uk.ac.man.bioinf.sequence.Element[])"><B>printElements(Element[])</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#printNode(uk.ac.man.bioinf.apps.xml.ConfigNode)"><B>printNode(ConfigNode)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#printNode(uk.ac.man.bioinf.apps.xml.ConfigNode, int)"><B>printNode(ConfigNode, int)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#printReport()"><B>printReport()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html#printSeq(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>printSeq(GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html">GappableSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html#printSeq(uk.ac.man.bioinf.sequence.Sequence)"><B>printSeq(Sequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html">EditableSequenceTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.complex.ComplexSequence)"><B>printSequence(ComplexSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.complex.GappedComplexSequence)"><B>printSequence(GappedComplexSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>printSequence(GappedSequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.Sequence)"><B>printSequence(Sequence)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#processingInstruction(java.lang.String, java.lang.String)"><B>processingInstruction(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#processItemEvent(java.awt.event.ItemEvent)"><B>processItemEvent(ItemEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#PROLINE"><B>PROLINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#propertiesEnd()"><B>propertiesEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#propertiesStart()"><B>propertiesStart()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html">CinemaStatusInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/Install.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html">Install</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#propertyChange(java.beans.PropertyChangeEvent)"><B>propertyChange(PropertyChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#props"><B>props</B></A> -
+Variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>ProteinResidue</B></A> - interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A>.<DD>ProteinResidue.java
+
+ An interface to represent a protein residue.<DT><A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>ProteinSequenceType</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A>.<DD>ProteinSequenceType.java
+
+
+ Created: Fri Mar 3 16:12:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#provideEnd()"><B>provideEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#push(java.lang.Object)"><B>push(Object)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_R_"><!-- --></A><H2>
+<B>R</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html#read()"><B>read()</B></A> -
+Method in class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html">NarrowedInputStream</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#readEnd()"><B>readEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>ReaderSource</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html">ReaderSource</A>.<DD>ReaderSource.java
+
+ This class identify the specific reader which was used to load the
+ identifiable object.<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html#ReaderSource(java.io.Reader)"><B>ReaderSource(Reader)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html">ReaderSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#readonly"><B>readonly</B></A> -
+Variable in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html"><B>ReadonlyException</B></A> - exception uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A>.<DD>ReadonlyException.java
+
+
+ Created: Thu Dec 14 15:40:59 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException()"><B>ReadonlyException()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>ReadonlyException(JAlignmentViewer)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException(java.lang.String)"><B>ReadonlyException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException(java.lang.String, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><B>ReadonlyException(String, JAlignmentViewer)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#readStart(org.xml.sax.Attributes)"><B>readStart(Attributes)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#recalculateIfInsetsChanged()"><B>recalculateIfInsetsChanged()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#registerKey(int, int)"><B>registerKey(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#registerKey(java.lang.String, int)"><B>registerKey(String, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#remember"><B>remember</B></A> -
+Variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#remove()"><B>remove()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#remove(int)"><B>remove(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#remove(int)"><B>remove(int)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Removes a module identifier at a specific index.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#remove(int)"><B>remove(int)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Removes a module at a specific index.
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#remove(int)"><B>remove(int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#remove(int, int)"><B>remove(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html">FormattedDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#remove(int, int)"><B>remove(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#remove(uk.ac.man.bioinf.module.Module)"><B>remove(Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Removes a module from the list.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#remove(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>remove(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Removes a module identifier from the list.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Delegates to the AlignmentListenerSupport the removal of the
+ MS listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>Removes a listener from the Vector.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>
+<DD>Removes a multiple sequence alignment listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><B>removeAlignmentListener(AlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>removeAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>removeAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>removeAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>removeAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><B>removeAlignmentSelectionListener(AlignmentSelectionListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html">AlignmentSelectionListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAll(java.util.Collection)"><B>removeAll(Collection)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAll(java.lang.Object[])"><B>removeAll(Object[])</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>Removes all the elements of this array from the list modely
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAll(java.util.Vector)"><B>removeAll(Vector)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAllElements()"><B>removeAllElements()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#removeButton(java.lang.String)"><B>removeButton(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>remove a menu with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html#removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><B>removeChangeListener(ChangeableListener)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/Changeable.html#removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><B>removeChangeListener(ChangeableListener)</B></A> -
+Method in interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Changeable.html">Changeable</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#removeChangeListener(javax.swing.event.ChangeListener)"><B>removeChangeListener(ChangeListener)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>
+<DD>Remove the listener from this cursor
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#removeChangeListener(javax.swing.event.ChangeListener)"><B>removeChangeListener(ChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#removeChangeListener(javax.swing.event.ChangeListener)"><B>removeChangeListener(ChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html">ChangeListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeCinemaPropertyChangeListener(java.beans.PropertyChangeListener)"><B>removeCinemaPropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><B>removeCinemaPropertyChangeListener(String, PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#removeComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><B>removeComplexElement(ComplexElement, Modification)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#removeComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><B>removeComplexElement(ComplexElement, Modification)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#removeConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><B>removeConsensusSequence(ConsensusSequence)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#removeCursorChangeListener(javax.swing.event.ChangeListener)"><B>removeCursorChangeListener(ChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#removeDebugInstance(uk.ac.man.bioinf.debug.DebugInterface)"><B>removeDebugInstance(DebugInterface)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>Remove a DebugInterface instance from the multiplexer.
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeElement(java.lang.Object)"><B>removeElement(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeElementAt(int)"><B>removeElementAt(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html#removeFromArray(java.lang.Object[], java.lang.Object[], java.lang.Object)"><B>removeFromArray(Object[], Object[], Object)</B></A> -
+Static method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html">ArrayManipulation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#removeGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><B>removeGroup(CinemaGroup)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#removeItemListener(java.awt.event.ItemListener)"><B>removeItemListener(ItemListener)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#removeListDataListener(javax.swing.event.ListDataListener)"><B>removeListDataListener(ListDataListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">AlignmentToListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#removeMenu(java.lang.String)"><B>removeMenu(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>remove a menu with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#removeMenuItem(java.lang.String)"><B>removeMenuItem(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>remove a menu item with the specified text label.
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><B>removeModificationAt(Modification, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><B>removeModificationAt(Modification, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>removeOptionable(Optionable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>removeOptionable(Optionable)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>
+<DD>Remove the following optionable object from
+ the list
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>removeOptionable(Optionable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html">NullOptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#removePropertyChangeListener(java.beans.PropertyChangeListener)"><B>removePropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#removePropertyChangeListener(java.beans.PropertyChangeListener)"><B>removePropertyChangeListener(PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><B>removePropertyChangeListener(String, PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><B>removePropertyChangeListener(String, PropertyChangeListener)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeRange(int, int)"><B>removeRange(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#removeSequence(int)"><B>removeSequence(int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Removes a sequence from the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeSequence(int)"><B>removeSequence(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequence(int)"><B>removeSequence(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Removes a sequence from the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeSequence(int)"><B>removeSequence(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)"><B>removeSequenceFromGroup(Sequence)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>
+<DD>Removes a sequence from this group
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)"><B>removeSequenceFromGroup(Sequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)"><B>removeSequenceFromGroup(Sequence)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>Removes a sequence listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><B>removeSequenceListener(SequenceListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>
+<DD>Removes the specified sequence listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#removeSequenceQuietly(int)"><B>removeSequenceQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Removes a sequence from the alignment, quietly, i.e., without
+ notifying any listeners.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequenceQuietly(int)"><B>removeSequenceQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Remove a sequence from the alignment, quietly, without notifying
+ listeners.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><B>removeSystemEventListener(SystemListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><B>removeSystemEventListener(SystemListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><B>removeSystemEventListener(SystemListener)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Delegates to the AlignmentListenerSupport the removal of the
+ vetoable MS listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html">AlignmentListenerSupport</A>
+<DD>Removes a vetoable alignment listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>
+<DD>Removes a vetoable multiple sequence alignment listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><B>removeVetoableAlignmentListener(VetoableAlignmentListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>Removes a vetoable sequence listener.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><B>removeVetoableSequenceListener(VetoableSequenceListener)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>
+<DD>Removes the specified vetoable sequence listener.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html#renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>renderAlignmentSelection(Graphics, int, int, int, int, JAlignmentViewer, SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html">DefaultAlignmentSelectionRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html#renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>renderAlignmentSelection(Graphics, int, int, int, int, JAlignmentViewer, SequenceAlignmentRectangle)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html">TextFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html">DefaultFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html">CursorLessFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html">ColorFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><B>renderAlignmentViewerCell(Graphics, int, int, int, int, JAlignmentViewer, Element, SequenceAlignmentPoint, Color, boolean, boolean, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html">BorderFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#renderCell(java.awt.Graphics, int, int, int, int, java.awt.Rectangle, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, uk.ac.man.bioinf.sequence.Element)"><B>renderCell(Graphics, int, int, int, int, Rectangle, SequenceAlignmentPoint, Element)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#repaint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>repaint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>requestOptionUpdate(Optionable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>requestOptionUpdate(Optionable)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>
+<DD>Request that the optionable object set the the options
+ of the optionable object via its setOptions method.
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)"><B>requestOptionUpdate(Optionable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html">NullOptionHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Residue.html"><B>Residue</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Residue.html">Residue</A>.<DD>Residue.java
+
+ An interface to represent entirely biological elements.<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#resize(int, int)"><B>resize(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Allows the resize of the dimension
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#resizeSelection(java.lang.String, uk.ac.man.bioinf.util.Direction, int)"><B>resizeSelection(String, Direction, int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#resolveClassName(java.lang.String)"><B>resolveClassName(String)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveClassName(java.lang.String)"><B>resolveClassName(String)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Resolves a classname of a module into the module identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#resolveClassName(java.lang.String)"><B>resolveClassName(String)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#resolveModuleName(java.lang.String)"><B>resolveModuleName(String)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveModuleName(java.lang.String)"><B>resolveModuleName(String)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Resolve a module name into a ModuleIdentifier
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#resolveModuleName(java.lang.String)"><B>resolveModuleName(String)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>This method resolves a module name into a ModuleIdentifier.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#resolveModuleName(java.lang.String)"><B>resolveModuleName(String)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#resolveXMLLoadName(java.lang.String)"><B>resolveXMLLoadName(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#resolveXMLLoadName(java.lang.String)"><B>resolveXMLLoadName(String)</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html">CinemaResources</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#resolveXMLLoadName(java.lang.String)"><B>resolveXMLLoadName(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html"><B>ResourceAdapter</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>.<DD>Generic class for locating resources within an application/applet's package
+ hierarchy.<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#ResourceAdapter()"><B>ResourceAdapter()</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html#ResourceAdapter(java.lang.String)"><B>ResourceAdapter(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>retrieveSequence(String, ParserExceptionHandler)</B></A> -
+Method in interface uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>retrieveSequence(String, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#retrieveSequenceStream(java.lang.String)"><B>retrieveSequenceStream(String)</B></A> -
+Method in interface uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#retrieveSequenceStream(java.lang.String)"><B>retrieveSequenceStream(String)</B></A> -
+Method in class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#RIGHT"><B>RIGHT</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>RNANucleotide</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>.<DD>RNANucleotide.java
+
+ A class for the representation of RNA Nucleotides.<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNAResidue.html"><B>RNAResidue</B></A> - interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A>.<DD>RNAResidue.java
+
+ An interface to represent an RNA Residue
+
+ Created: Mon Feb 28 13:02:16 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html"><B>RNASequenceType</B></A> - class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A>.<DD>RNASequenceType.java
+
+
+ Created: Mon Nov 27 16:02:20 2000<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html#RNASequenceType()"><B>RNASequenceType()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#run()"><B>run()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#run()"><B>run()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#runStart()"><B>runStart()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_S_"><!-- --></A><H2>
+<B>S</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html"><B>SaveableOptions</B></A> - class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>.<DD>SaveableOptions.java
+
+ This class is used to initilise and save all of the necessary
+ options required.<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#SaveableOptions(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)"><B>SaveableOptions(SystemEventProducer, OptionableExceptionHandler)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>saveAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html">FileSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>saveAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>saveAlignmentAs(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html">FileSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>saveAlignmentAs(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#sendStatusMessage(java.lang.String)"><B>sendStatusMessage(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#sendStatusMessage(java.lang.String)"><B>sendStatusMessage(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>Send a message to the status bar.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html#SEQ_ALIGN"><B>SEQ_ALIGN</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html">CinemaProperties</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html#SEQ_INPUT"><B>SEQ_INPUT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html#SEQ_OUTPUT"><B>SEQ_OUTPUT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#sequence"><B>sequence</B></A> -
+Variable in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Sequence.html"><B>Sequence</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>.<DD>Sequence.java
+
+ This interface is designed to model a biological sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> - interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>.<DD>SequenceAlignment.java
+
+ This interface is designed to mimic a biological sequence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html"><B>SequenceAlignmentDimension</B></A> - class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>.<DD>SequenceAlignmentDimension.java
+
+ Represents a dimension within a SA.<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#SequenceAlignmentDimension()"><B>SequenceAlignmentDimension()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#SequenceAlignmentDimension(int, int)"><B>SequenceAlignmentDimension(int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#SequenceAlignmentDimension(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><B>SequenceAlignmentDimension(SequenceAlignmentDimension)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>SequenceAlignmentPoint</B></A> - class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>.<DD>SequenceAlignmentPoint.java
+
+ Represents a point in an alignment, where X is the position in a
+ sequence, and Y is the index of the sequence in the alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#SequenceAlignmentPoint()"><B>SequenceAlignmentPoint()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#SequenceAlignmentPoint(int, int)"><B>SequenceAlignmentPoint(int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#SequenceAlignmentPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>SequenceAlignmentPoint(SequenceAlignmentPoint)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html"><B>SequenceAlignmentRectangle</B></A> - class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>.<DD>SequenceAlignmentRectangle.java
+
+ Defines a rectangular region in a sequence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle()"><B>SequenceAlignmentRectangle()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(int, int, int, int)"><B>SequenceAlignmentRectangle(int, int, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(int, int, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><B>SequenceAlignmentRectangle(int, int, SequenceAlignmentDimension)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int, int)"><B>SequenceAlignmentRectangle(SequenceAlignmentPoint, int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>SequenceAlignmentRectangle(SequenceAlignmentRectangle)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html"><B>SequenceAlignmentShape</B></A> - interface uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A>.<DD>SequenceAlignmentShape.java
+
+ Defines a shape used to identify a region in a sequence alignment.<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html"><B>SequenceAlignmentTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A>.<DD>SequenceAlignmentTest.java
+
+
+ Created: Fri Mar 10 12:39:40 2000<DT><A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html"><B>SequenceAlignmentToChangeableAdaptor</B></A> - class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A>.<DD>SequenceAlignmentToChangeableAdaptor.java
+
+
+ Created: Thu Jul 20 17:57:44 2000<DT><A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#SequenceAlignmentToChangeableAdaptor(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>SequenceAlignmentToChangeableAdaptor(SequenceAlignment)</B></A> -
+Constructor for class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html"><B>SequenceCharacterIterator</B></A> - class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html">SequenceCharacterIterator</A>.<DD>SequenceCharacterIterator.java
+
+ This class provides the link between the sequence package and
+ jakarta regexp package.<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#SequenceCharacterIterator(uk.ac.man.bioinf.sequence.Sequence)"><B>SequenceCharacterIterator(Sequence)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html">SequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>SequenceColumnTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html">SequenceColumnTest</A>.<DD>SequenceColumnTest.java
+
+
+ Created: Wed Jun 7 15:41:17 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html#SequenceColumnTest()"><B>SequenceColumnTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html">SequenceColumnTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html"><B>SequenceCursor</B></A> - interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>.<DD>SequenceCursor.java
+
+
+ Created: Mon Apr 3 18:59:26 2000<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html"><B>SequenceEvent</B></A> - class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>.<DD>SequenceEvent.java
+
+ Instances of this class represent an event to a sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html#SequenceEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><B>SequenceEvent(Object, int, int, SequenceEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>
+<DD>Constructor to set the event source, location and type, which allows
+ the definition of the start and end of an event.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html#SequenceEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><B>SequenceEvent(Object, int, SequenceEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>
+<DD>Constructor to set the event source, location and type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>SequenceEventProvider</B></A> - interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>.<DD>SequenceEventProvider.java
+
+ An interface designed to enforce the methods necessary to listen to a
+ sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html"><B>SequenceEventType</B></A> - class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>.<DD>SequenceEventType.java
+
+ This class provides an enumerated type for the SequenceEvent class
+ to pass around as an identifier
+
+ Created: Tue Feb 15 20:10:48 2000<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceException.html"><B>SequenceException</B></A> - exception uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceException.html">SequenceException</A>.<DD>SequenceException.java
+
+
+ Created: Thu Mar 2 17:07:48 2000<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceException.html#SequenceException(java.lang.String)"><B>SequenceException(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceException.html">SequenceException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>SequenceFactory</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>.<DD>SequenceFactory provides a simple way into the Sequence API.<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html#SequenceFactory()"><B>SequenceFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html">SequenceFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html"><B>SequenceFactoryTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html">SequenceFactoryTest</A>.<DD>SequenceFactoryTest.java
+
+
+ Created: Tue Nov 14 18:21:42 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html#SequenceFactoryTest()"><B>SequenceFactoryTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html">SequenceFactoryTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html"><B>SequenceGroup</B></A> - interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A>.<DD>SequenceGroup.java
+
+ This interface defines a SequenceGroup that is capable of storing a
+ collection of sequences.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html"><B>SequenceInputModuleIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A>.<DD>A module interface identifier for sequence input.<DT><A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html"><B>SequenceInputParser</B></A> - interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/ [...]
+
+ This class defines the basic interface for parsing sequence files.<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>SequenceListener</B></A> - interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>.<DD>SequenceListener.java
+
+ Listens for events occuring to a sequence<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html"><B>SequenceListenerSupport</B></A> - class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>.<DD>SequenceListenerSupport.java
+
+ This class provides support and handles the listeners to a specific
+ sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#SequenceListenerSupport()"><B>SequenceListenerSupport()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html">SequenceListenerSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html"><B>SequenceOutputModuleIdentifier</B></A> - class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A>.<DD>SequenceOutputModuleIdentifier.java
+
+
+ Created: Fri Aug 11 15:06:07 2000<DT><A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html"><B>SequenceRetriever</B></A> - interface uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>.<DD>SequenceRetriever.java
+
+
+ Created: Thu Feb 8 16:42:01 2001<DT><A HREF="uk/ac/man/bioinf/sequence/Sequences.html"><B>Sequences</B></A> - class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequences.html">Sequences</A>.<DD>Sequences.java
+
+
+ Created: Tue Mar 14 13:43:59 2000<DT><A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html"><B>SequenceSearch</B></A> - class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html">SequenceSearch</A>.<DD>SequenceSearch.java
+
+ Searches through a SequenceAlignment specified on the command line for
+ all occurrences of the given regexp.<DT><A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html#SequenceSearch()"><B>SequenceSearch()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/SequenceSearch.html">SequenceSearch</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>SequenceSource</B></A> - interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A>.<DD>SequenceSource.java
+
+ This class represents the source that is used to produce a
+ sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html"><B>SequencesTest</B></A> - class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html">SequencesTest</A>.<DD>SequencesTest.java
+
+
+ Created: Tue Mar 14 14:19:44 2000<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html#SequencesTest()"><B>SequencesTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequencesTest.html">SequencesTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html"><B>SequenceType</B></A> - interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>.<DD>SequenceType.java
+
+ An interface to represent the type of a sequence (e.g: Protein, DNA).<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html"><B>SequenceVetoException</B></A> - exception uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>.<DD>SequenceVetoException.java
+
+ An exception thrown when an object vetos a sequence change event.<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html#SequenceVetoException(java.lang.String, uk.ac.man.bioinf.sequence.event.SequenceEvent)"><B>SequenceVetoException(String, SequenceEvent)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>
+<DD>The constructor; storing the event as well as source
+<DT><A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html"><B>SequenceWriterException</B></A> - exception uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html">SequenceWriterException</A>.<DD>An exception cast when an IOException is thrown in writing the
+ sequence out from CINEMA.<DT><A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html#SequenceWriterException()"><B>SequenceWriterException()</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html">SequenceWriterException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#SERINE"><B>SERINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html#SET"><B>SET</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#set(int, int)"><B>set(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#set(int, java.lang.Object)"><B>set(int, Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#setAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)"><B>setAlignmentSelectionModel(AlignmentSelectionModel)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)"><B>setAlignmentSelectionModel(AlignmentSelectionModel)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setAlignmentSelectionRenderer(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer)"><B>setAlignmentSelectionRenderer(AlignmentSelectionRenderer)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#setBottomLeft(javax.swing.JComponent)"><B>setBottomLeft(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setBounds(int, int, int, int)"><B>setBounds(int, int, int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the boundry defined by this region.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><B>setBounds(SequenceAlignmentPoint, SequenceAlignmentDimension)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the boundry defined by this region.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><B>setBounds(SequenceAlignmentRectangle)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the boundry defined by this region.
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setButton(uk.ac.man.bioinf.sequence.alignment.GappedSequence, javax.swing.JButton)"><B>setButton(GappedSequence, JButton)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCellHeight(int)"><B>setCellHeight(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCellRenderer(uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer)"><B>setCellRenderer(AlignmentViewerCellRenderer)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setCellsSquare(boolean)"><B>setCellsSquare(boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCellWidth(int)"><B>setCellWidth(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#setColor(java.awt.Color)"><B>setColor(Color)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)"><B>setColorMap(ColorMap)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)"><B>setColorMap(ColorMap)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)"><B>setColorMap(ColorMap)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>Changes the color map and notifies of change.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#setColumn(int)"><B>setColumn(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html">AlignmentColumn</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#setComplexElementFactory(uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface)"><B>setComplexElementFactory(ComplexElementFactoryInterface)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html">ComplexElementFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>setConcreteIdentifier(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)"><B>setConcreteIdentifier(ModuleIdentifier, ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)"><B>setConcreteIdentifier(ModuleIdentifier, ModuleIdentifier)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Set the concrete identifier for a given abstract identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)"><B>setConcreteIdentifier(ModuleIdentifier, ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><B>setConfig(ModuleIdentifier, Object)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><B>setConfig(ModuleIdentifier, Object)</B></A> -
+Method in interface uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>
+<DD>Sets the config to a particular module described by an identifier.
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><B>setConfig(ModuleIdentifier, Object)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#setConfig(java.lang.Object)"><B>setConfig(Object)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>setConsensusCalculator(ConsensusCalculator)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>setConsensusCalculator(ConsensusCalculator)</B></A> -
+Method in interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#setContents(javax.swing.JComponent)"><B>setContents(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#setContext(uk.ac.man.bioinf.module.ModuleContext)"><B>setContext(ModuleContext)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#setContext(uk.ac.man.bioinf.module.ModuleContext)"><B>setContext(ModuleContext)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#setCursorBlink()"><B>setCursorBlink()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCursorModel(uk.ac.man.bioinf.gui.viewer.SequenceCursor)"><B>setCursorModel(SequenceCursor)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#setData(uk.ac.man.bioinf.module.ModuleIdentifier)"><B>setData(ModuleIdentifier)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html#setData(java.lang.String)"><B>setData(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>
+<DD>Set the data for this config node.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setDecimalFieldValue(java.lang.String, double)"><B>setDecimalFieldValue(String, double)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setDefaultDividerLocation(int)"><B>setDefaultDividerLocation(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#setDefaultInvokerInternalQueue(uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)"><B>setDefaultInvokerInternalQueue(InvokerInternalQueue)</B></A> -
+Static method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultLocation(int, int)"><B>setDefaultLocation(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Pretty much the same as setDefaultSize
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setDefaultOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><B>setDefaultOptionHandler(OptionHandler)</B></A> -
+Static method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><B>setDefaultOptionHandler(OptionHandler)</B></A> -
+Static method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultSize(int, int)"><B>setDefaultSize(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>This sets the size of the frame, only if it hasnt been set as an option.
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#setDocumentLocator(org.xml.sax.Locator)"><B>setDocumentLocator(Locator)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><B>setElementAt(Element[], int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><B>setElementAt(Element[], int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>Provides a simple implementation of this method by iterating
+ through the element array, and calling the super class
+ method.
+<DT><A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element, int)"><B>setElementAt(Element, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>
+<DD>Sets the value of the element at the specified index.
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element, int)"><B>setElementAt(Element, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#setElementAt(java.lang.Object, int)"><B>setElementAt(Object, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)"><B>setElementAtQuietly(ComplexElement, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)"><B>setElementAtQuietly(ComplexElement, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)"><B>setElementAtQuietly(ComplexElement, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><B>setElementAtQuietly(Element, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><B>setElementAtQuietly(Element, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#setExceptionHandler(uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler)"><B>setExceptionHandler(AbstractSequenceParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#setExceptionHandler(uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler)"><B>setExceptionHandler(AbstractSequenceParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>
+<DD>Sets the parser exception handler.
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html#setExceptionHandler(uk.ac.man.bioinf.util.ExceptionHandler)"><B>setExceptionHandler(ExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setFastCellRenderer(uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)"><B>setFastCellRenderer(FastAlignmentViewerCellRenderer)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setFixedCellHeight(int)"><B>setFixedCellHeight(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#setFrameTitle(java.lang.String)"><B>setFrameTitle(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#setInset(int, int)"><B>setInset(int, int)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>
+<DD>Sets the inset of a sequence within the alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#setInset(int, int)"><B>setInset(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setInset(int, int)"><B>setInset(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Set the inset (or number of preceeding gaps) in a sequence.
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#setInset(int, int)"><B>setInset(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#setInsetQuietly(int, int)"><B>setInsetQuietly(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#setInsetQuietly(int, int)"><B>setInsetQuietly(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>Sets the inset (or preceeding number of gaps) for a sequence in the
+ alignment.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setInsetQuietly(int, int)"><B>setInsetQuietly(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>Set the inset (or number of preceeding gaps) in a sequence, quietly
+ without notifying listeners.
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#setInstance(uk.ac.man.bioinf.debug.DebugInterface)"><B>setInstance(DebugInterface)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#setInstance(java.lang.String)"><B>setInstance(String)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setIntegerFieldValue(java.lang.String, int)"><B>setIntegerFieldValue(String, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setJAlignmentViewer()"><B>setJAlignmentViewer()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#setLengthQuietly(int)"><B>setLengthQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#setLengthQuietly(int)"><B>setLengthQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setLengthQuietly(int)"><B>setLengthQuietly(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setLocation(int, int)"><B>setLocation(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the progom location of the rectangle.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setLocation(int, int)"><B>setLocation(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Sets the location of the point.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setLocation(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>setLocation(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the origin location of the rectangle.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setLocation(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>setLocation(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>Sets the location of the point.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#setMainWindow(javax.swing.JComponent)"><B>setMainWindow(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#setMark()"><B>setMark()</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>
+<DD>Set the mark to the current position of point
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setMark()"><B>setMark()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#setMark()"><B>setMark()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#setMenuEnabled(java.lang.String, boolean)"><B>setMenuEnabled(String, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#setMenuItemEnabled(java.lang.String, boolean)"><B>setMenuItemEnabled(String, boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setModifierType(java.lang.String, int)"><B>setModifierType(String, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html">PedanticColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html">NullColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html">WhiteColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html">IntenseColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html">GrayScaleVariance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><B>setModule(CinemaModule)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html#setModule(uk.ac.man.bioinf.module.Module)"><B>setModule(Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#setModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module)"><B>setModule(ModuleIdentifier, Module)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleContext.html#setModuleFactory(uk.ac.man.bioinf.module.ModuleFactoryInstance)"><B>setModuleFactory(ModuleFactoryInstance)</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#setNameForSelection(java.lang.String, java.lang.String)"><B>setNameForSelection(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#setOneAtATime(boolean)"><B>setOneAtATime(boolean)</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>Set the value of oneAtATime.
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><B>setOptionHandler(OptionHandler)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>
+<DD>Set the value of OptionHandler.
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><B>setOptionHandler(OptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><B>setOptionHandler(OptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Implementation of the OptionableInterface
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setOptions()"><B>setOptions()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptions()"><B>setOptions()</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#setOptions(java.lang.Object)"><B>setOptions(Object)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)"><B>setOptions(Object)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>
+<DD>Sets the options for this object
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setOptions(java.lang.Object)"><B>setOptions(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptions(java.lang.Object)"><B>setOptions(Object)</B></A> -
+Method in class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>
+<DD>Implementation of the Optionable Interface.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#setPassword(java.lang.String)"><B>setPassword(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>setPoint(SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>
+<DD>Set the point to the new position
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>setPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>setPoint(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#setPreferredWidthPerBase(int)"><B>setPreferredWidthPerBase(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setReadonly(boolean)"><B>setReadonly(boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#setRememberPassword(boolean)"><B>setRememberPassword(boolean)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)"><B>setSelectionModel(AlignmentSelectionModel)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setSequenceAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>Set the Sequence Alignment.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setSequenceAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setSequenceAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setSequenceAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setSequenceAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>setSequenceAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)"><B>setSequenceColor(GappedSequence, Color)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)"><B>setSequenceTitleColor(GappedSequence, Color)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>
+<DD>This sets the colour that is used to display the sequence
+ title.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)"><B>setSequenceTitleColor(GappedSequence, Color)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#setSize(int)"><B>setSize(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setSize(int, int)"><B>setSize(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the size of the rectangle.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#setSize(int, int)"><B>setSize(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Sets the size of the dimension.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setSize(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><B>setSize(SequenceAlignmentDimension)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>Sets the size of the rectangle.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#setSize(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><B>setSize(SequenceAlignmentDimension)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A>
+<DD>Sets the size of the dimension.
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)"><B>setSource(Source)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)"><B>setSource(Source)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)"><B>setSource(Source)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setTextFieldValue(java.lang.String, java.lang.String)"><B>setTextFieldValue(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#setTitle(java.lang.String)"><B>setTitle(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#setTopLeft(javax.swing.JComponent)"><B>setTopLeft(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setUI(uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI)"><B>setUI(AlignmentViewerUI)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#setUI(javax.swing.plaf.SliderUI)"><B>setUI(SliderUI)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#setUserName(java.lang.String)"><B>setUserName(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html#setValue(double)"><B>setValue(double)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">DecimalField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#setValue(int)"><B>setValue(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">WholeNumberField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html#setValue(int)"><B>setValue(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setX(int)"><B>setX(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setXCellsPerPage(int)"><B>setXCellsPerPage(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>Set the number of cells which should be drawn across each page.
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setY(int)"><B>setY(int)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setYCellsPerPage(int)"><B>setYCellsPerPage(int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A>
+<DD>Set the number of cells which should be drawn down each page.
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#show()"><B>show()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html#show(java.awt.Component, java.net.URL)"><B>show(Component, URL)</B></A> -
+Static method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html">PopUpHtmlDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#showInitialSplash()"><B>showInitialSplash()</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html#showMessage(java.lang.String)"><B>showMessage(String)</B></A> -
+Method in class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">ApplicationFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html#showSlaveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><B>showSlaveAlignment(SequenceAlignment)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html">CinemaSlaveViewerModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>SimpleIdentifier</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html">SimpleIdentifier</A>.<DD>SimpleIdentifier.java
+
+
+ Created: Wed Jul 5 19:30:33 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html#SimpleIdentifier(java.lang.String)"><B>SimpleIdentifier(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html">SimpleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html#SimpleIdentifier(java.lang.String, uk.ac.man.bioinf.sequence.identifier.Source)"><B>SimpleIdentifier(String, Source)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html">SimpleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html"><B>SimpleSource</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">SimpleSource</A>.<DD>SimpleSource.java
+
+ Utility class mainly meant to extend from.<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html#SimpleSource(java.lang.String)"><B>SimpleSource(String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">SimpleSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>SingleAlignmentSelectionModel</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>.<DD>SingleAlignmentSelectionModel.java
+
+
+ Created: Mon Apr 10 11:59:44 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#SingleAlignmentSelectionModel()"><B>SingleAlignmentSelectionModel()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>SingleColorMap</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html">SingleColorMap</A>.<DD>SingleColorMap.java
+
+ This class is designed to return one color, regardless of the
+ element being displayed.<DT><A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html#SingleColorMap(java.awt.Color)"><B>SingleColorMap(Color)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html">SingleColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html#SingleColorMap(java.awt.Color, java.lang.String)"><B>SingleColorMap(Color, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html">SingleColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>SingleSelectionModelTest</B></A> - class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html">SingleSelectionModelTest</A>.<DD>SingleSelectionModelTest.java
+
+
+ Created: Wed Apr 12 17:34:46 2000<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html#SingleSelectionModelTest()"><B>SingleSelectionModelTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html">SingleSelectionModelTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html"><B>SingleSequenceAlignment</B></A> - class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html">SingleSequenceAlignment</A>.<DD>SingleSequenceAlignment.java
+
+ This class is for those stick occasions when you want a
+ SequenceAlignment but all you have is a Sequence.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html#SingleSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><B>SingleSequenceAlignment(GappedSequence)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html">SingleSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>SingletonModification</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/SingletonModification.html">SingletonModification</A>.<DD>SingletonModification.java
+
+
+ Created: Mon Feb 28 23:16:04 2000<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Returns the number of module identifiers.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Returns the number of modules.
+<DT><A HREF="uk/ac/man/bioinf/sequence/SequenceType.html#size()"><B>size()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>
+<DD>Returns the number of elements in this sequence type.
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#size()"><B>size()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#skippedEntity(java.lang.String)"><B>skippedEntity(String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html"><B>SliderExample</B></A> - class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html">SliderExample</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html#SliderExample()"><B>SliderExample()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html">SliderExample</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#slow()"><B>slow()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#slowImpl()"><B>slowImpl()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#sort()"><B>sort()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>Sort the contents of this list.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#sortMotifs()"><B>sortMotifs()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html"><B>Source</B></A> - interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>.<DD>SequenceSource.java
+
+ This class represents the source that is used to produce a
+ sequence.<DT><A HREF="uk/ac/man/bioinf/util/Direction.html#SOUTH"><B>SOUTH</B></A> -
+Static variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Direction.html">Direction</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html">CinemaMenuSystem</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html">CinemaGo</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html">CinemaStatusInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/Module.html#start()"><B>start()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html">Module</A>
+<DD>The method called externally to initiate the modules function.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html#startCinemaInstance()"><B>startCinemaInstance()</B></A> -
+Static method in class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html">Cinema</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#startDocument()"><B>startDocument()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)"><B>startElement(String, String, String, Attributes)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#startEnd()"><B>startEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#startPrefixMapping(java.lang.String, java.lang.String)"><B>startPrefixMapping(String, String)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html#stateChanged(javax.swing.event.ChangeEvent)"><B>stateChanged(ChangeEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html">BasicAlignmentViewerUI.PointListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>stopSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>stopSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>stopSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>stopSelection(SequenceAlignmentPoint)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><B>stopSelection(SequenceAlignmentPoint)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>
+<DD>Complete the selection at the given point
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#storeException(uk.ac.man.bioinf.io.ParserException)"><B>storeException(ParserException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A>
+<DD>Stores the exception, so that later a call can be made to
+ getParserExceptions() in order to display all the exceptions
+ together.
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#storeException(uk.ac.man.bioinf.io.ParserException)"><B>storeException(ParserException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A>
+<DD>Stores the exception, so that later a call can be made to
+ getParserExceptions() in order to display all the exceptions
+ together.
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>StreamSequenceSource</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A>.<DD>StreamSequenceSource.java
+
+
+ Created: Tue Jul 4 17:30:29 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#StreamSequenceSource(java.io.Reader, java.lang.String)"><B>StreamSequenceSource(Reader, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#stripGapsFromElements(uk.ac.man.bioinf.sequence.Element[], int)"><B>stripGapsFromElements(Element[], int)</B></A> -
+Static method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#substring(int)"><B>substring(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html">SequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#substring(int)"><B>substring(int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#substring(int, int)"><B>substring(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html">SequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#substring(int, int)"><B>substring(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#swap(int, int)"><B>swap(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html">SwappingListBasicUI.SwappingMouseInputHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#swapGroupOrder(int, int)"><B>swapGroupOrder(int, int)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>SwappingListBasicUI</B></A> - class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html">SwappingListBasicUI</A>.<DD>SwappingListBasicUI.java
+
+ This class enables dragging of list items around something like
+ XMMS's playlist.<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html"><B>SwappingListBasicUI.SwappingMouseInputHandler</B></A> - class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html">SwappingListBasicUI.SwappingMouseInputHandler</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#SwappingListBasicUI.SwappingMouseInputHandler()"><B>Swap [...]
+Constructor for class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html">SwappingListBasicUI.SwappingMouseInputHandler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#SwappingListBasicUI()"><B>SwappingListBasicUI()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html">SwappingListBasicUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>SwissProtIdentifier</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html">SwissProtIdentifier</A>.<DD>SwissProtIdentifier.java
+
+
+ Created: Wed Jul 5 14:16:55 2000<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html#SwissProtIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, java.lang.String)"><B>SwissProtIdentifier(Source, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html">SwissProtIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html#SYSTEM_SHUTDOWN"><B>SYSTEM_SHUTDOWN</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#systemClosing"><B>systemClosing</B></A> -
+Variable in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html"><B>SystemEvent</B></A> - class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A>.<DD>SystemEvent.java
+
+
+ <DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html#SystemEvent(java.lang.Object, uk.ac.man.bioinf.apps.systemevents.SystemEventOption)"><B>SystemEvent(Object, SystemEventOption)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><B>systemEventOccured(SystemEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><B>systemEventOccured(SystemEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><B>systemEventOccured(SystemEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><B>systemEventOccured(SystemEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>
+<DD>This is an event listener for system events.
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>SystemEventOption</B></A> - class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A>.<DD>SystemEventOption.java
+
+
+ <DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html"><B>SystemEventProducer</B></A> - interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A>.<DD>SystemEventProducer.java
+
+ Interface defining the SystemEventProducer
+
+ Created: Fri Oct 01 14:55:42 1999<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html"><B>SystemEventSupport</B></A> - class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A>.<DD>SystemEventSupport.java
+
+ Provides a basic queue for holding all the listeners.<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#SystemEventSupport()"><B>SystemEventSupport()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html"><B>SystemListener</B></A> - interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>.<DD>SystemListener.java
+
+ Listeners to system events.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#systemListenerPriority()"><B>systemListenerPriority()</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#systemListenerPriority()"><B>systemListenerPriority()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#systemListenerPriority()"><B>systemListenerPriority()</B></A> -
+Method in class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemListenerPriority()"><B>systemListenerPriority()</B></A> -
+Method in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>
+<DD>Some events (particularly shut downs) have to happen in a
+ very specific order.
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html"><B>SystemVetoException</B></A> - exception uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A>.<DD>SystemVetoException.java
+
+
+ Created: Thu Apr 15 17:23:20 1999<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html#SystemVetoException(java.lang.String, uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><B>SystemVetoException(String, SystemEvent)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_T_"><!-- --></A><H2>
+<B>T</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>TaylorColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#TaylorColorMapMetaData()"><B>TaylorColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html">TaylorColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html"><B>TextFastAlignmentViewerCellRenderer</B></A> - class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html">TextFastAlignmentViewerCellRenderer</A>.<DD>TextFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer.<DT><A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html#TextFastAlignmentViewerCellRenderer()"><B>TextFastAlignmentViewerCellRenderer()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html">TextFastAlignmentViewerCellRenderer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html#THIAMINE"><B>THIAMINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html"><B>ThreadableColorMap</B></A> - interface uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A>.<DD>ThreadableColorMap.java
+
+ Defines a color map that can perform any necessary calculations to
+ in a thread safe manner.<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html"><B>ThreadedColorMap</B></A> - class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>.<DD>ThreadedColorMap.java
+
+ This class implements the threaded functionality for ColorMap.<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#ThreadedColorMap(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.color.ThreadableColorMap)"><B>ThreadedColorMap(JAlignmentViewer, SequenceAlignment, ThreadableColorMap)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#ThreadedColorMap(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.color.ThreadableColorMap, uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)"><B>ThreadedColorMap(JAlignmentViewer, SequenceAlignment, ThreadableColorMap, InvokerInternalQueue)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html"><B>ThreadedConsensusSequence</B></A> - class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>.<DD>ThreadedConsensusSequence.java
+
+ This class calls the calculation out of the event thread, so that
+ background analysis is made more easily.<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#ThreadedConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>ThreadedConsensusSequence(ConsensusCalculator)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#ThreadedConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator, uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)"><B>ThreadedConsensusSequence(ConsensusCalculator, InvokerInternalQueue)</B></A> -
+Constructor for class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html"><B>ThreadedPercentageIDConsensusCalculatorMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A>.<DD>ThreadedPercentageIDConsensusCalculatorMetaData.java
+
+
+ Created: Wed Nov 8 15:01:52 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#ThreadedPercentageIDConsensusCalculatorMetaData()"><B>ThreadedPercentageIDConsensusCalculatorMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>ThreadedPercentageIDVarianceColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A>.<DD>ThreadedPercentageIDVarianceColorMapMetaData.java
+
+
+ Created: Fri Dec 1 16:54:24 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#ThreadedPercentageIDVarianceColorMapMetaData()"><B>ThreadedPercentageIDVarianceColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#THREONINE"><B>THREONINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/NullDebug.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/NullDebug.html">NullDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultFileDebug.html">DefaultFileDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html">DefaultDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)"><B>throwable(Class, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html#throwable(java.lang.Object, java.lang.Throwable)"><B>throwable(Object, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Object, java.lang.Throwable)"><B>throwable(Object, Throwable)</B></A> -
+Method in interface uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/Debug.html#throwable(java.lang.Object, java.lang.Throwable)"><B>throwable(Object, Throwable)</B></A> -
+Static method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html">Debug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Object, java.lang.Throwable)"><B>throwable(Object, Throwable)</B></A> -
+Method in class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#toArray()"><B>toArray()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html#toArray()"><B>toArray()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A>
+<DD>Returns an array of module identifiers.
+<DT><A HREF="uk/ac/man/bioinf/module/ModuleList.html#toArray()"><B>toArray()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A>
+<DD>Returns an array of modules.
+<DT><A HREF="uk/ac/man/bioinf/util/IntArrayList.html#toArray()"><B>toArray()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/Element.html#toChar()"><B>toChar()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Element.html">Element</A>
+<DD>Returns a character representation of this element.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html#toChar()"><B>toChar()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html#toChar()"><B>toChar()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html#toChar()"><B>toChar()</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#toChar()"><B>toChar()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#toElements(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>toElements(String, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#toGappedMap"><B>toGappedMap</B></A> -
+Variable in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#toList()"><B>toList()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#toSequence(uk.ac.man.bioinf.sequence.identifier.Identifier, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>toSequence(Identifier, String, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html#toSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>toSequence(String, String, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()"><B>toString()</B></A> -
+Method in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#treeEnd()"><B>treeEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#treeStart()"><B>treeStart()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#trimToSize()"><B>trimToSize()</B></A> -
+Method in class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html"><B>TripletPanel</B></A> - class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>.<DD>Triplet panel provides a GUI Component with three sub components.<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#TripletPanel()"><B>TripletPanel()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html#TripletPanel(javax.swing.JComponent, javax.swing.JComponent, javax.swing.JComponent)"><B>TripletPanel(JComponent, JComponent, JComponent)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">TripletPanel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#TRYPTOPHAN"><B>TRYPTOPHAN</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#TYROSINE"><B>TYROSINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_U_"><!-- --></A><H2>
+<B>U</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#uiClassID"><B>uiClassID</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#uiClassID"><B>uiClassID</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/package-summary.html"><B>uk.ac.man.bioinf</B></A> - package uk.ac.man.bioinf<DD> <DT><A HREF="uk/ac/man/bioinf/analysis/consensus/package-summary.html"><B>uk.ac.man.bioinf.analysis.consensus</B></A> - package uk.ac.man.bioinf.analysis.consensus<DD> <DT><A HREF="uk/ac/man/bioinf/analysis/misc/package-summary.html"><B>uk.ac.man.bioinf.analysis.misc</B></A> - package uk.ac.man.bioinf.analysis.misc<DD> <DT><A HREF="uk/ac/man/bioinf/analysis/regexp [...]
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#unanchorGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><B>unanchorGroup(CinemaGroup)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#uninstallAlignmentListners(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><B>uninstallAlignmentListners(ConsensusCalculator)</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#uninstallListeners()"><B>uninstallListeners()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#uninstallUI(javax.swing.JComponent)"><B>uninstallUI(JComponent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/UnknownElementException.html"><B>UnknownElementException</B></A> - exception uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A>.<DD>An exception to flag an unrecognised element in a string.<DT><A HREF="uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(int)"><B>UnknownElementException(int)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(int, java.lang.String)"><B>UnknownElementException(int, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(java.lang.String, int)"><B>UnknownElementException(String, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(java.lang.String, int, java.lang.String)"><B>UnknownElementException(String, int, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(java.lang.String, int, java.lang.String, uk.ac.man.bioinf.sequence.identifier.Identifier)"><B>UnknownElementException(String, int, String, Identifier)</B></A> -
+Constructor for class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#unsetCursorBlink()"><B>unsetCursorBlink()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#UNSPECIFIED"><B>UNSPECIFIED</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A>
+<DD>This type says that the alignment has changed in some unknown
+ way.
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html#UNSPECIFIED"><B>UNSPECIFIED</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#UP"><B>UP</B></A> -
+Static variable in class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#updateUI()"><B>updateUI()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#updateUI()"><B>updateUI()</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html#URACIL"><B>URACIL</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html"><B>URLSequenceSource</B></A> - class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html">URLSequenceSource</A>.<DD>URLSequenceSource.java
+
+ A source for a sequence stored at a URL.<DT><A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html#URLSequenceSource(java.net.URL, java.lang.String)"><B>URLSequenceSource(URL, String)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html">URLSequenceSource</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#userName"><B>userName</B></A> -
+Variable in class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html">PasswordDialog</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_V_"><!-- --></A><H2>
+<B>V</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#validate()"><B>validate()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#validate()"><B>validate()</B></A> -
+Method in class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#validate()"><B>validate()</B></A> -
+Method in class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html">ThreadedColorMap</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html"><B>ValidatedForm</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#ValidatedForm()"><B>ValidatedForm()</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">ValidatedForm</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html#VALINE"><B>VALINE</B></A> -
+Static variable in class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><B>valueChanged(AlignmentSelectionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><B>valueChanged(AlignmentSelectionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><B>valueChanged(AlignmentSelectionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><B>valueChanged(AlignmentSelectionEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#valueChanged(javax.swing.event.ListSelectionEvent)"><B>valueChanged(ListSelectionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#valueChanged(javax.swing.event.ListSelectionEvent)"><B>valueChanged(ListSelectionEvent)</B></A> -
+Method in class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#valueEnd()"><B>valueEnd()</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>VariableColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#VariableColorMapMetaData()"><B>VariableColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html">VariableColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>VariationsColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#VariationsColorMapMetaData()"><B>VariationsColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html">VariationsColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html"><B>VersionInformation</B></A> - class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>.<DD>VersionInformation.java
+
+ This provides standard information about this version of Cinema.<DT><A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#VersionInformation()"><B>VersionInformation()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html">VersionInformation</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_ERROR"><B>VETO_DUE_TO_ERROR</B></A> -
+Static variable in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>
+<DD>This value should be used when the System shutdown can
+ not be aborted unless there is some error in the shutdown
+ procedure
+<DT><A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_USER_REQUEST"><B>VETO_DUE_TO_USER_REQUEST</B></A> -
+Static variable in interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>
+<DD>This value should be used when the user has full control
+ over aborting the shutdown.
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html"><B>VetoableAlignmentEvent</B></A> - class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A>.<DD>VetoableAlignmentEvent.java
+
+ An event that may be vetoed by a listener.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html#VetoableAlignmentEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><B>VetoableAlignmentEvent(Object, int, AlignmentEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html#VetoableAlignmentEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><B>VetoableAlignmentEvent(Object, int, int, AlignmentEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><B>VetoableAlignmentListener</B></A> - interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A>.<DD>VetoableAlignmentListener.java
+
+ Listeners of this type are informed before a change takes place,
+ and throw an exception if they so wish.<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><B>vetoableChangeOccurred(VetoableAlignmentEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A>
+<DD>Method called before a change occurs to an alignment
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><B>vetoableChangeOccurred(VetoableAlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><B>vetoableChangeOccurred(VetoableAlignmentEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>vetoableChangeOccurred(VetoableSequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>vetoableChangeOccurred(VetoableSequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>vetoableChangeOccurred(VetoableSequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>vetoableChangeOccurred(VetoableSequenceEvent)</B></A> -
+Method in interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A>
+<DD>Method signalled before a prospective change occurs
+<DT><A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><B>vetoableChangeOccurred(VetoableSequenceEvent)</B></A> -
+Method in class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html"><B>VetoableSequenceEvent</B></A> - class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A>.<DD>VetoableSequenceEvent.java
+
+
+ Created: Fri Feb 18 17:38:50 2000<DT><A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html#VetoableSequenceEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><B>VetoableSequenceEvent(Object, int, int, SequenceEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html#VetoableSequenceEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><B>VetoableSequenceEvent(Object, int, SequenceEventType)</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><B>VetoableSequenceListener</B></A> - interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A>.<DD>VetoableSequenceListener.java
+
+ When a sequence wishes to change it should signal listeners of this
+ type first before it makes the change.</DL>
+<HR>
+<A NAME="_W_"><!-- --></A><H2>
+<B>W</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#warning(org.xml.sax.SAXParseException)"><B>warning(SAXParseException)</B></A> -
+Method in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html"><B>WeakModificationSetFactory</B></A> - class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A>.<DD>WeakModificationSetFactory.java
+
+
+ Created: Wed Mar 1 15:09:49 2000<DT><A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#WeakModificationSetFactory()"><B>WeakModificationSetFactory()</B></A> -
+Constructor for class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/util/Direction.html#WEST"><B>WEST</B></A> -
+Static variable in class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Direction.html">Direction</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>WhiteColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html">WhiteColorMapMetaData</A>.<DD>WhiteColorMapMetaData.java
+
+
+ Created: Fri Feb 9 13:12:26 2001<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#WhiteColorMapMetaData()"><B>WhiteColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html">WhiteColorMapMetaData</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>WholeNumberField</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">WholeNumberField</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html"><B>WholeNumberField.WholeNumberDocument</B></A> - class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html">W [...]
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html">WholeNumberField.WholeNumberDocument</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#WholeNumberField(int, int)"><B>WholeNumberField(int, int)</B></A> -
+Constructor for class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">WholeNumberField</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html#windowClosing(java.awt.event.WindowEvent)"><B>windowClosing(WindowEvent)</B></A> -
+Method in class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html">BasicWindowMonitor</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>write(SequenceAlignment, Writer, ParserExceptionHandler)</B></A> -
+Method in interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A>
+<DD>Returns a writer for output, when provided with a sequence
+ alignment.
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>write(SequenceAlignment, Writer, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A>
+<DD>This method parses a sequence alignment and writes it out to the
+ supplied writer.
+<DT><A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)"><B>write(SequenceAlignment, Writer, ParserExceptionHandler)</B></A> -
+Method in class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/MotProteinParser.html">MotProteinParser</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_X_"><!-- --></A><H2>
+<B>X</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html#XML_BOOT"><B>XML_BOOT</B></A> -
+Static variable in class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html">XMLBootIdentifier</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html"><B>XMLBootIdentifier</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html">XMLBootIdentifier</A>.<DD>XMLBootIdentifier.java
+
+
+ Created: Thu May 25 11:57:19 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>XMLBootModule</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>.<DD>XMLBootModule.java
+
+ This is a module which loads other modules by parsing an XML file
+ defined by the module DTD.<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>XMLBootModule.MiniStack</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A>.<DD> <DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#XMLBootModule.MiniStack()"><B>XMLBootModule.MiniStack()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html#XMLBootModule()"><B>XMLBootModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>XMLBootParserListener</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>.<DD>XMLBootParserListener.java
+
+
+ Created: Tue May 9 22:10:53 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#XMLBootParserListener(uk.ac.man.bioinf.apps.xml.XMLBootModule)"><B>XMLBootParserListener(XMLBootModule)</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html">XMLBootParserListener</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html"><B>XMLLoadingTest</B></A> - class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A>.<DD>XMLLoadingTest.java
+
+
+ Created: Tue May 16 12:35:51 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#XMLLoadingTest()"><B>XMLLoadingTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A> - class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A>.<DD>XMLModule.java
+
+ This class provides configuration information specific to the
+ XMLModules.<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html#XMLModule()"><B>XMLModule()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A>
+<DD>
+<DT><A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html"><B>XMLParserFactory</B></A> - interface uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A>.<DD>XMLParserFactory.java
+
+
+ Created: Mon Sep 18 18:52:56 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html"><B>XMLStartTest</B></A> - class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html">XMLStartTest</A>.<DD>XMLStartTest.java
+
+
+ Created: Thu May 25 12:05:07 2000<DT><A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html#XMLStartTest()"><B>XMLStartTest()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html">XMLStartTest</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_Y_"><!-- --></A><H2>
+<B>Y</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/Y.html"><B>Y</B></A> - class uk.ac.man.bioinf.<A HREF="uk/ac/man/bioinf/Y.html">Y</A>.<DD>Y.java
+
+ Class created entirely for the purpose of being tab
+ completable.<DT><A HREF="uk/ac/man/bioinf/Y.html#Y()"><B>Y()</B></A> -
+Constructor for class uk.ac.man.bioinf.<A HREF="uk/ac/man/bioinf/Y.html">Y</A>
+<DD>
+</DL>
+<HR>
+<A NAME="_Z_"><!-- --></A><H2>
+<B>Z</B></H2>
+<DL>
+<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html"><B>ZenecaColorMapMetaData</B></A> - class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>.<DD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000<DT><A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#ZenecaColorMapMetaData()"><B>ZenecaColorMapMetaData()</B></A> -
+Constructor for class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A>
+<DD>
+</DL>
+<HR>
+<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_J_">J</A> <A HREF="#_K_">K</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <A HREF="#_X_">X</A> <A HREF=" [...]
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="index-all.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/index.html b/doc/javadoc/index.html
new file mode 100644
index 0000000..a9f660d
--- /dev/null
+++ b/doc/javadoc/index.html
@@ -0,0 +1,25 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:07 BST 2002-->
+<TITLE>
+Generated Documentation (Untitled)
+</TITLE>
+</HEAD>
+<FRAMESET cols="20%,80%">
+<FRAMESET rows="30%,70%">
+<FRAME src="overview-frame.html" name="packageListFrame">
+<FRAME src="allclasses-frame.html" name="packageFrame">
+</FRAMESET>
+<FRAME src="overview-summary.html" name="classFrame">
+</FRAMESET>
+<NOFRAMES>
+<H2>
+Frame Alert</H2>
+
+<P>
+This document is designed to be viewed using the frames feature. If you see this message, you are using a non-frame-capable web client.
+<BR>
+Link to<A HREF="overview-summary.html">Non-frame version.</A></NOFRAMES>
+</HTML>
diff --git a/doc/javadoc/overview-frame.html b/doc/javadoc/overview-frame.html
new file mode 100644
index 0000000..811b48b
--- /dev/null
+++ b/doc/javadoc/overview-frame.html
@@ -0,0 +1,134 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+Overview ()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Overview ()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameTitleFont">
+<B></B></FONT></TD>
+</TR>
+</TABLE>
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="allclasses-frame.html" TARGET="packageFrame">All Classes</A></FONT>
+<P>
+<FONT size="+1" CLASS="FrameHeadingFont">
+Packages</FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/analysis/consensus/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.analysis.consensus</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/analysis/misc/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.analysis.misc</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/analysis/regexp/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.analysis.regexp</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/color/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.color</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.consensus</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/core/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.core</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.core.test</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/group/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.group</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/io/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.io</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/motif/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.motif</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/resources/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.resources</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/shared/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.shared</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/cinema/utils/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.cinema.utils</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/commandline/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.commandline</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/invoker/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.invoker</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/optionable/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.optionable</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/systemevents/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.systemevents</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/xml/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.xml</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/apps/xml/test/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.apps.xml.test</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/database/fetch/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.database.fetch</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/debug/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.debug</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/color/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.color</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/misc/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.misc</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/optionable/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.optionable</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/util/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.util</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/util/forms/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.util.forms</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/viewer/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.viewer</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/viewer/event/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.viewer.event</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.viewer.plaf</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/gui/viewer/test/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.gui.viewer.test</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/io/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.io</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/io/parsers/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.io.parsers</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/io/test/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.io.test</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/module/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.module</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/alignment/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.alignment</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/alignment/event/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.alignment.event</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/complex/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.complex</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/event/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.event</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/geom/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.geom</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/group/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.group</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/identifier/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.identifier</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/test/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.test</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/sequence/types/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.sequence.types</A></FONT>
+<BR>
+<FONT CLASS="FrameItemFont"><A HREF="uk/ac/man/bioinf/util/package-frame.html" TARGET="packageFrame">uk.ac.man.bioinf.util</A></FONT>
+<BR>
+</TD>
+</TR>
+</TABLE>
+
+<P>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/overview-summary.html b/doc/javadoc/overview-summary.html
new file mode 100644
index 0000000..1349992
--- /dev/null
+++ b/doc/javadoc/overview-summary.html
@@ -0,0 +1,341 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:07 BST 2002 -->
+<TITLE>
+Overview ()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Overview ()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="overview-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Sequence Packages</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/package-summary.html">uk.ac.man.bioinf.sequence</A></B></TD>
+<TD>Provides classes for representing mutable sequences.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/alignment/package-summary.html">uk.ac.man.bioinf.sequence.alignment</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/alignment/event/package-summary.html">uk.ac.man.bioinf.sequence.alignment.event</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/complex/package-summary.html">uk.ac.man.bioinf.sequence.complex</A></B></TD>
+<TD>Provides complex sequence support.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/event/package-summary.html">uk.ac.man.bioinf.sequence.event</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/geom/package-summary.html">uk.ac.man.bioinf.sequence.geom</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/group/package-summary.html">uk.ac.man.bioinf.sequence.group</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/identifier/package-summary.html">uk.ac.man.bioinf.sequence.identifier</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/test/package-summary.html">uk.ac.man.bioinf.sequence.test</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/sequence/types/package-summary.html">uk.ac.man.bioinf.sequence.types</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Gui Packages</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/color/package-summary.html">uk.ac.man.bioinf.gui.color</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/misc/package-summary.html">uk.ac.man.bioinf.gui.misc</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/optionable/package-summary.html">uk.ac.man.bioinf.gui.optionable</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/util/package-summary.html">uk.ac.man.bioinf.gui.util</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/util/forms/package-summary.html">uk.ac.man.bioinf.gui.util.forms</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/viewer/package-summary.html">uk.ac.man.bioinf.gui.viewer</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/viewer/event/package-summary.html">uk.ac.man.bioinf.gui.viewer.event</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html">uk.ac.man.bioinf.gui.viewer.plaf</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/gui/viewer/test/package-summary.html">uk.ac.man.bioinf.gui.viewer.test</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Cinema</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/package-summary.html">uk.ac.man.bioinf.apps.cinema</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/color/package-summary.html">uk.ac.man.bioinf.apps.cinema.color</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html">uk.ac.man.bioinf.apps.cinema.consensus</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/core/package-summary.html">uk.ac.man.bioinf.apps.cinema.core</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html">uk.ac.man.bioinf.apps.cinema.core.test</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/group/package-summary.html">uk.ac.man.bioinf.apps.cinema.group</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/io/package-summary.html">uk.ac.man.bioinf.apps.cinema.io</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/motif/package-summary.html">uk.ac.man.bioinf.apps.cinema.motif</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/resources/package-summary.html">uk.ac.man.bioinf.apps.cinema.resources</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/shared/package-summary.html">uk.ac.man.bioinf.apps.cinema.shared</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/cinema/utils/package-summary.html">uk.ac.man.bioinf.apps.cinema.utils</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Other Packages</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/package-summary.html">uk.ac.man.bioinf</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/analysis/consensus/package-summary.html">uk.ac.man.bioinf.analysis.consensus</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/analysis/misc/package-summary.html">uk.ac.man.bioinf.analysis.misc</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/analysis/regexp/package-summary.html">uk.ac.man.bioinf.analysis.regexp</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/commandline/package-summary.html">uk.ac.man.bioinf.apps.commandline</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/invoker/package-summary.html">uk.ac.man.bioinf.apps.invoker</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/optionable/package-summary.html">uk.ac.man.bioinf.apps.optionable</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/systemevents/package-summary.html">uk.ac.man.bioinf.apps.systemevents</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/xml/package-summary.html">uk.ac.man.bioinf.apps.xml</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/apps/xml/test/package-summary.html">uk.ac.man.bioinf.apps.xml.test</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/database/fetch/package-summary.html">uk.ac.man.bioinf.database.fetch</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/debug/package-summary.html">uk.ac.man.bioinf.debug</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/io/package-summary.html">uk.ac.man.bioinf.io</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/io/parsers/package-summary.html">uk.ac.man.bioinf.io.parsers</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/io/test/package-summary.html">uk.ac.man.bioinf.io.test</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/module/package-summary.html">uk.ac.man.bioinf.module</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="20%"><B><A HREF="uk/ac/man/bioinf/util/package-summary.html">uk.ac.man.bioinf.util</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+<P>
+ <HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Overview</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="overview-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/overview-tree.html b/doc/javadoc/overview-tree.html
new file mode 100644
index 0000000..fca8922
--- /dev/null
+++ b/doc/javadoc/overview-tree.html
@@ -0,0 +1,517 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:11:52 BST 2002 -->
+<TITLE>
+Class Hierarchy ()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Class Hierarchy ()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="overview-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For All Packages</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="uk/ac/man/bioinf/package-tree.html">uk.ac.man.bioinf</A>, <A HREF="uk/ac/man/bioinf/analysis/consensus/package-tree.html">uk.ac.man.bioinf.analysis.consensus</A>, <A HREF="uk/ac/man/bioinf/analysis/misc/package-tree.html">uk.ac.man.bioinf.analysis.misc</A>, <A HREF="uk/ac/man/bioinf/analysis/regexp/package-tree.html">uk.ac.man.bioinf.analysis.regexp</A>, <A HREF="uk/ac/man/bioinf/apps/cinema/package-tree.html">uk.ac.man.bioinf.apps.cinema</A>, [...]
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/AbstractDebug.html"><B>AbstractDebug</B></A> (implements uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>CinemaDebug.DebugImpl</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>CinemaDebug.DebugImpl</B></A><LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DefaultDebug.html"><B>DefaultDebug</B></A><LI TYPE="circle">class uk.ac.man.bioinf.de [...]
+<LI TYPE="circle">class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html"><B>AbstractDocument</B></A> (implements javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html"><B>PlainDocument</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>FormattedDocument</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>IntegerField.IntegerDocument</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html"><B>WholeNumberField.WholeNumberD [...]
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractElement.html"><B>AbstractElement</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>AminoAcid</B></A> (implements uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>DNANucleotide</B></A> (implements uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>RNANucleotide</B></A> (implements uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>CinemaBootIdentifier</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>CinemaColorIdentifier</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>CinemaCommandLineParserIdentifier</B></A [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>CinemaProperties</B></A><LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Direction.html"><B>Direction</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>ModuleExceptionType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/Sequ [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>AbstractEnumeration.ElementIterator</B></A> (implements java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html"><B>AbstractGappedSequenceGroup</B></A> (implements uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>DefaultGappedSequenceGroup</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html"><B>GroupSequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bio [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>CinemaGroup</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html"><B>AbstractIdentifier</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html"><B>ConsensusIdentifier</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>DatabaseIdentifier</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>SwissProtIdentifier</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>SimpleIdentifier</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html"><B>AbstractListModel</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>AlignmentToListModel</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html"><B>ChunkyListModel</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.AbstractModification (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>SingletonModification</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>Methylation</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html"><B>AbstractProteinAlignmentInputParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html"><B>PIRProteinAlignmentParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>AbstractProteinSequenceInputParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>FastaSequenceParser</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>AbstractSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>AbstractMutableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html"><B>AbstractComplexSequence</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>DefaultComplexSequence</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>DefaultGappedComplexSequence</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/AbstractEditableSequence.html"><B>AbstractEditableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>DefaultEditableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html"><B>AbstractGappedSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>DefaultConsensusSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, uk.ac.man.bioinf.sequence.event.<A HREF= [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html"><B>ThreadedConsensusSequence</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>DefaultGappedSequence</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>DefaultSequence</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>AbstractSequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>DefaultSequenceAlignment</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html"><B>SingleSequenceAlignment</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>AbstractSequenceInputParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>FileSequenceInputParserExceptionHandler</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>AbstractSequenceParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>FileSequenceParserExceptionHandler</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>AbstractSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>AbstractComplexSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>AbstractEnumeratedSequenceType</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>DNASequenceType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>ProteinSequenceType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNASequenceType.html"><B>RNASequenceType</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>AlignmentColumn</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>AlignmentEventType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>AlignmentListener [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ArrayManipulation.html"><B>ArrayManipulation</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>BasicAlignmentViewerUI.KeyScroller</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>BasicAlignmentViewerUI.PointListener</B></A> (implements javax.swing.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>BasicAlignmentViewerUI.SelectionClearer</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>BasicAlignmentViewerUI.SelectionToggler</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html"><B>BasicListUI.MouseInputHandler</B></A> (implements javax.swing.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html"><B>SwappingListBasicUI.SwappingMouseInputHandler</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html"><B>BorderFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>ButtonPanelTest</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html"><B>CalculatePercentageID</B></A><LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>ChangeableListenerSupport</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html"><B>SequenceAlignmentToChangeableAdaptor</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/Changeable.html">Changeable</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListe [...]
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html"><B>ChangeListenerSupport</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>CheckMotifLocationAgainstPrints</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/Cinema.html"><B>Cinema</B></A><LI TYPE="circle">class uk.ac [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>CinemaFileOptionableExceptionHandler</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>CinemaGroupManager</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html"><B>CinemaResources</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html"><B>CinemaTestLaunch</B></A><LI TYPE="circl [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/CollectionPrinter.html"><B>CollectionPrinter</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>ColorFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorGenerator.html"><B>ColorGenerator</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorList.html"><B>ColorList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>ColormapColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/ [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorStore.html"><B>ColorStore</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html"><B>ComplexElementAndModificationTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>ComplexElementFactory</B></A><LI TYPE="circle">class uk. [...]
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html"><B>CellRendererPane</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>CellRendererPaneReplacement</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>JAlignmentViewer</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/ [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>PrintableJAlignmentViewer</B></A> (implements java.awt.print.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html">Printable</A>)
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html"><B>JLabel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>DefaultAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html"><B>DefaultListCellRenderer</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListCellRenderer.html">ListCellRenderer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html"><B>AlignmentToListCellRenderer</B></A></UL>
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html"><B>JPanel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>JAlignmentButtonPanel</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/ItemSelectable.html">ItemSelectable</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>PrintableAlignmentPanel</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html"><B>SliderExample</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html"><B>TripletPanel</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/a [...]
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html"><B>JPopupMenu</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/MenuElement.html">MenuElement</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>ButtonViewerPopupMenu</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A>)
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html"><B>JScrollPane</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>JChangedScrollPane</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>JLayableScrollPane</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html"><B>JSlider</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>JAlignmentRuler</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html"><B>JSplitPane</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html"><B>OptionableJSplitPane</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>)
+</UL>
+<LI TYPE="circle">class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html"><B>JTextComponent</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Scrollable.html">Scrollable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html"><B>JTextField</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html"><B>DecimalField</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>IntegerField</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>WholeNumberField</B></A></UL>
+</UL>
+</UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html"><B>AlignmentViewerTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html"><B>ApplicationFrame</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html"><B>CinemaMotifFrame</B></A> (implements java.awt.event.<A HREF="http://java. [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.optionable.<A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>OptionableJFrame</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html"><B>CinemaAlignmentFrame</B></A> (implements java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>CinemaGroupFrame</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, javax.swing.event.<A HREF="http://java.sun.com/products/jdk/ [...]
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html"><B>ComponentUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html"><B>AlignmentRulerUI</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>AlignmentViewerUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>BasicAlignmentViewerUI</B></A> (implements javax.swing.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html"><B>MetalAlignmentViewerUI</B></A></UL>
+</UL>
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ListUI.html"><B>ListUI</B></A><UL>
+<LI TYPE="circle">class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html"><B>BasicListUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.misc.<A HREF="uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>SwappingListBasicUI</B></A></UL>
+</UL>
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/SliderUI.html"><B>SliderUI</B></A><UL>
+<LI TYPE="circle">class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html"><B>BasicSliderUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>BasicAlignmentRulerUI</B></A></UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/ConfigNode.html"><B>ConfigNode</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html"><B>ConsensusPercentageIDColorMap</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.gui.color.<A HREF="u [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/Debug.html"><B>Debug</B></A><LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>DebugMultiplexer</B></A> (implements uk.ac.man.bioinf.debug.<A HREF="uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>DefaultAlignmentSelectionRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>DefaultColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>DefaultComplexElement</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>DefaultComplexSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>DefaultFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>DefaultModuleFactoryInstance</B></A> (implements uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>CinemaModuleFactoryInstance</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html"><B>DefaultParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>DefaultSequenceCursor</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>DefaultXMLParser</B></A> (implements uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html"><B>DoubleArrayColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html"><B>EditableSequenceTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>EmptyGappedSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EmptySequence.html"><B>EmptySequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>EmptySequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>EmptySequenceType</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>)
+<LI TYPE="circle">class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html"><B>EventObject</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html"><B>AlignmentEvent</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html"><B>VetoableAlignmentEvent</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html"><B>AlignmentSelectionEvent</B></A><LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html"><B>ChangeableEvent</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html"><B>SequenceEvent</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html"><B>VetoableSequenceEvent</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html"><B>SystemEvent</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html"><B>ExpasySequenceRetriever</B></A> (implements uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html"><B>FetchSequenceBySwissProtID</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>FileSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>Gap</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Element.html">Element</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html"><B>GappableSequenceTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html"><B>GappedSequenceCharacterIterator</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.commandline.<A HREF="uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html"><B>GappedSequenceSearch</B></A>< [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>GrayScaleVariance</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>HardModificationSetFactory</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>IndividualElementColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>)
+<LI TYPE="circle">class java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html"><B>InputStream</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>NarrowedInputStream</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/Install.html"><B>Install</B></A> (implements java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>InstancePerAlignmentColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/IntArrayList.html"><B>IntArrayList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>IntenseColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>Invoker</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/AnonInvoker.html"><B>AnonInvoker</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>InvokerInternalQueue</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A>, uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html"><B>InvokerThreadManager</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>Js_TestColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>ModificationFactory</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>CinemaCoreGui</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>CinemaDebug</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html"><B>CinemaDebug</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>CinemaInvoker</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>CinemaSharedQuitExit</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>CinemaSystemEvents</B></A> (implements uk.ac.man.bioi [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>XMLBootModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>CinemaBoot</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>CinemaShared</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>CinemaColorFactory</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>CinemaCommandLineParser</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html"><B>CinemaConsensus</B></A><LI TYPE="circl [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html"><B>AbstractSequenceInput</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>FileSequenceInput</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>AbstractSequenceOutput</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>FileSequenceOutput</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>CinemaColorSelector</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>CinemaConsensusDisplay</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>CinemaCoreView</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>CinemaGo</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>CinemaMenuSystem</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>CinemaSequenceMenu</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinem [...]
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>CinemaMenuBuilder</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>CinemaMotifModule</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>CinemaMultipleConsensusViewer</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>CinemaPersist</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>CinemaFilePersist</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>CinemaRegexp</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>CinemaResizeElements</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>CinemaSlaveViewerModule</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html"><B>CinemaSplash</B></A></UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleContext.html"><B>ModuleContext</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>DefaultModuleContext</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>ModuleIdentifierList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleList.html"><B>ModuleList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>ModuleStorageStructure</B></A><LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="uk/ac/man/bioinf/io/parsers/Mo [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>MultiplexerFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>CursorLessFastAlignmentViewerCellRenderer</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html"><B>NamedAlignmentSelectionModel</B></A> (implements uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>NoIdentifier</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>NoSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>NullAlignmentSelectionModel</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>NullColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/NullModuleFactory.html"><B>NullModuleFactory</B></A> (implements uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html"><B>XMLLoadingTest</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>NullOptionHandler</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/NullParserExceptionHandler.html"><B>NullParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>PasswordDialog</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>PedanticColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html"><B>PercentageIDCalculator</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.misc.<A HREF="uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html"><B>PercentageIDCalculatorManager</B></A><LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>PercentageIDConsensus</B></A> (implements uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>PercentageIDConsensusCalculatorMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html"><B>ThreadedPercentageIDConsensusCalculatorMetaData</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>PercentageIDVarianceColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>PercentIDVarianceColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.<A HREF="uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>PopUpHtmlDisplay</B></A><LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ResourceAdapter.html"><B>ResourceAdapter</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>PackageResourceAdapter</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/SaveableOptions.html"><B>SaveableOptions</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>, uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html"><B>FileSaveableOptions</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html"><B>ScrollPaneLayout</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/LayoutManager.html">LayoutManager</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable. [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>InvertedScrollPaneLayout</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html"><B>SequenceAlignmentDimension</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>SequenceAlignmentPoint</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Cloneable.html">Cloneable</A>, java.lang.<A HREF="http://java.sun.com/products/jdk [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html"><B>SequenceAlignmentRectangle</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A>, uk.ac.man.bioinf.sequence.geom.<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html"><B>SequenceAlignmentTest</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioin [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.regexp.<A HREF="uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html"><B>SequenceCharacterIterator</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>SequenceColumnTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>SequenceFactory</B></A><LI TYPE="circle">class uk.ac.man.bioinf.se [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>ReaderSource</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>SingleAlignmentSelectionModel</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>SingleColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>SingleSelectionModelTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>StreamSequenceSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html"><B>URLSequenceSource</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>SystemEventOption</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html"><B>SystemEventSupport</B></A> (implements uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>TaylorColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html"><B>TextFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadedColorMap.html"><B>ThreadedColorMap</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">Prop [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>ThreadedPercentageIDVarianceColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html"><B>AlignmentVetoException</B></A><LI TYPE="circle">class java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html"><B>IOException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html"><B>OptionableSourceNotFoundException</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="uk/ac/man/bioinf/module/ModuleException.html"><B>ModuleException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html"><B>OptionableStateException</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html"><B>ColorMapException</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html"><B>IllegalArgumentException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html"><B>MalformedAccessionException</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html"><B>IllegalDuplicateModificationException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html"><B>InvalidSequenceTypeException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html"><B>Inv [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html"><B>InvalidSequenceTypeParserException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html"><B>SequenceWriterException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/UnknownElementException.html"><B>UnknownElementException</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html"><B>ReadonlyException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/SequenceException.html"><B>SequenceException</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html"><B>SequenceVetoException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html"><B>SystemVetoException</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>VariableColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>VariationsColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html"><B>VersionInformation</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html"><B>WeakModificationSetFactory</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>WhiteColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html"><B>WindowAdapter</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowFocusListener.html">WindowFocusListener</A>, java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowListener.html">WindowListener</A>, java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/doc [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>BasicWindowMonitor</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>XMLBootModule.MiniStack</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>XMLBootParserListener</B></A> (implements org.xml.sax.ContentHandler, org.xml.sax.ErrorHandler)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.test.<A HREF="uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html"><B>XMLStartTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.<A HREF="uk/ac/man/bioinf/Y.html"><B>Y</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html"><B>ZenecaColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMet [...]
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html"><B>AlignmentEventProvider</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/e [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentInputParser.html"><B>AlignmentInputParser</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>AlignmentOutputParser</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html"><B>AlignmentSelectionModel</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.<A HREF [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.gui.color.<A HREF="uk/ac/man/bioinf/gui/color/ThreadableColorMap.html"><B>ThreadableColorMap</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html"><B>ColorMapMetaData</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>ComplexElementFactoryInterface</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html"><B>ConsensusCalcu [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexElement.html"><B>ComplexElement</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Residue.html"><B>Residue</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>NucleotideResidue</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/DNAResidue.html"><B>DNAResidue</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/RNAResidue.html"><B>RNAResidue</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>ProteinResidue</B></A></UL>
+</UL>
+<LI TYPE="circle">interface java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html"><B>EventListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>AlignmentListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><B>VetoableAlignmentListener</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.event.<A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html"><B>AlignmentSelectionListener</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>SequenceListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><B>VetoableSequenceListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac [...]
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemListener.html"><B>SystemListener</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.util.<A HREF="uk/ac/man/bioinf/util/ExceptionHandler.html"><B>ExceptionHandler</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html"><B>FastAlignmentViewerCellRenderer</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html"><B>Sequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gappe [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>ComplexSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html">M [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>)
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gappe [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html"><B>EditableSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSe [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html">Mut [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>ConsensusSequence</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>)
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>, uk.ac.man.bioinf.sequence.event.<A HRE [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>Identifier</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/Modification.html"><B>Modification</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html"><B>ModificationSetFactoryInterface</B></A><LI TYPE="c [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/Gappe [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html"><B>EditableSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSe [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="uk/ac/man/bioinf/sequence/MutableSequence.html">Mut [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.analysis.consensus.<A HREF="uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>ConsensusSequence</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>)
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.event.<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, uk.ac.man.bioinf.sequence.event.<A HREF="uk/ac [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/SequenceGroup.html"><B>SequenceGroup</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.group.<A HREF="uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html"><B>GappedSequenceGroup</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.io.<A HREF="uk/ac/man/bioinf/io/SequenceInputParser.html"><B>SequenceInputParser</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.database.fetch.<A HREF="uk/ac/man/bioinf/database/fetch/SequenceRetriever.html"><B>SequenceRetriever</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>SequenceSource</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequ [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>ComplexSequenceType</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="uk/ac/man/bioinf/sequence/identifier/Source.html"><B>Source</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.apps.systemevents.<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html"><B>SystemEventProducer</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.apps.xml.<A HREF="uk/ac/man/bioinf/apps/xml/XMLParserFactory.html"><B>XMLParserFactory</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="overview-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/package-list b/doc/javadoc/package-list
new file mode 100644
index 0000000..a924eee
--- /dev/null
+++ b/doc/javadoc/package-list
@@ -0,0 +1,47 @@
+uk.ac.man.bioinf
+uk.ac.man.bioinf.analysis.consensus
+uk.ac.man.bioinf.analysis.misc
+uk.ac.man.bioinf.analysis.regexp
+uk.ac.man.bioinf.apps.cinema
+uk.ac.man.bioinf.apps.cinema.color
+uk.ac.man.bioinf.apps.cinema.consensus
+uk.ac.man.bioinf.apps.cinema.core
+uk.ac.man.bioinf.apps.cinema.core.test
+uk.ac.man.bioinf.apps.cinema.group
+uk.ac.man.bioinf.apps.cinema.io
+uk.ac.man.bioinf.apps.cinema.motif
+uk.ac.man.bioinf.apps.cinema.resources
+uk.ac.man.bioinf.apps.cinema.shared
+uk.ac.man.bioinf.apps.cinema.utils
+uk.ac.man.bioinf.apps.commandline
+uk.ac.man.bioinf.apps.invoker
+uk.ac.man.bioinf.apps.optionable
+uk.ac.man.bioinf.apps.systemevents
+uk.ac.man.bioinf.apps.xml
+uk.ac.man.bioinf.apps.xml.test
+uk.ac.man.bioinf.database.fetch
+uk.ac.man.bioinf.debug
+uk.ac.man.bioinf.gui.color
+uk.ac.man.bioinf.gui.misc
+uk.ac.man.bioinf.gui.optionable
+uk.ac.man.bioinf.gui.util
+uk.ac.man.bioinf.gui.util.forms
+uk.ac.man.bioinf.gui.viewer
+uk.ac.man.bioinf.gui.viewer.event
+uk.ac.man.bioinf.gui.viewer.plaf
+uk.ac.man.bioinf.gui.viewer.test
+uk.ac.man.bioinf.io
+uk.ac.man.bioinf.io.parsers
+uk.ac.man.bioinf.io.test
+uk.ac.man.bioinf.module
+uk.ac.man.bioinf.sequence
+uk.ac.man.bioinf.sequence.alignment
+uk.ac.man.bioinf.sequence.alignment.event
+uk.ac.man.bioinf.sequence.complex
+uk.ac.man.bioinf.sequence.event
+uk.ac.man.bioinf.sequence.geom
+uk.ac.man.bioinf.sequence.group
+uk.ac.man.bioinf.sequence.identifier
+uk.ac.man.bioinf.sequence.test
+uk.ac.man.bioinf.sequence.types
+uk.ac.man.bioinf.util
diff --git a/doc/javadoc/packages.html b/doc/javadoc/packages.html
new file mode 100644
index 0000000..f2764f1
--- /dev/null
+++ b/doc/javadoc/packages.html
@@ -0,0 +1,26 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:07 BST 2002 -->
+<TITLE>
+
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<BODY BGCOLOR="white">
+
+<BR>
+
+<BR>
+
+<BR>
+<CENTER>
+The front page has been relocated.Please see:
+<BR>
+ <A HREF="index.html">Frame version</A>
+<BR>
+ <A HREF="overview-summary.html">Non-frame version.</A></CENTER>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/serialized-form.html b/doc/javadoc/serialized-form.html
new file mode 100644
index 0000000..0e09049
--- /dev/null
+++ b/doc/javadoc/serialized-form.html
@@ -0,0 +1,2735 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:40 BST 2002 -->
+<TITLE>
+Serialized Form
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Serialized Form";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="serialized-form.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H1>
+Serialized Form</H1>
+</CENTER>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.cinema.group</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+groupsList</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A> <B>groupsList</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+module</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> <B>module</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+groupsListModel</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A> <B>groupsListModel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+sequencesListModel</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">ChunkyListModel</A> <B>sequencesListModel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+viewGroupAlignment</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>viewGroupAlignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+editGroupName</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>editGroupName</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+addToConsensus</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>addToConsensus</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+createNewGroup</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>createNewGroup</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+addAllAsGroup</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>addAllAsGroup</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+anchor</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>anchor</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+unanchor</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>unanchor</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+anchorAll</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>anchorAll</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+unanchorAll</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>unanchorAll</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+lastSelectedGroup</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> <B>lastSelectedGroup</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.cinema.core</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html">uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html">uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+alignment</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>alignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.cinema.utils</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+mainPanel</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>mainPanel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+rulerPanel</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>rulerPanel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+rowHeadersPanel</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>rowHeadersPanel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+viewer</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>viewer</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+scrollPane</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>scrollPane</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+rowHeaders</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A> <B>rowHeaders</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+ruler</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A> <B>ruler</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+initialCellSize</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>initialCellSize</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.cinema.motif</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+selectionList</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A> <B>selectionList</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+sequencesList</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A> <B>sequencesList</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+selectionListModel</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListModel.html">DefaultListModel</A> <B>selectionListModel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+sequencesListModel</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListModel.html">DefaultListModel</A> <B>sequencesListModel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+plusNorth</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>plusNorth</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+plusEast</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>plusEast</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+plusSouth</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>plusSouth</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+plusWest</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>plusWest</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+minusNorth</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>minusNorth</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+minusEast</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>minusEast</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+minusSouth</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>minusSouth</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+minusWest</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>minusWest</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+quit</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>quit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+clearAll</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>clearAll</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+clearSelected</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>clearSelected</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+saveSelected</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>saveSelected</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+save</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>save</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+sortMotifs</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JCheckBox.html">JCheckBox</A> <B>sortMotifs</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+motifName</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A> <B>motifName</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+selectionRegion</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A> <B>selectionRegion</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+motifNameBorder</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/border/TitledBorder.html">TitledBorder</A> <B>motifNameBorder</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+model</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A> <B>model</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+module</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A> <B>module</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+abst</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A> <B>abst</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+exceptionHandler</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> <B>exceptionHandler</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+dirChooser</H3>
+<PRE>
+CinemaMotifFrame.MotifFormatFileChooser <B>dirChooser</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+fileChooser</H3>
+<PRE>
+CinemaMotifFrame.MotifFormatFileChooser <B>fileChooser</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.invoker</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html">uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+e</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> <B>e</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html">uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.optionable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.optionable.OptionableStateException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">uk.ac.man.bioinf.apps.optionable.OptionableStateException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.apps.systemevents</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.systemevents.SystemEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">uk.ac.man.bioinf.apps.systemevents.SystemEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+option</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> <B>option</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.apps.systemevents.SystemVetoException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">uk.ac.man.bioinf.apps.systemevents.SystemVetoException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+event</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> <B>event</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.color</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.color.ColorMapException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/color/ColorMapException.html">uk.ac.man.bioinf.gui.color.ColorMapException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.misc</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.misc.ChunkyListModel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/misc/ChunkyListModel.html">uk.ac.man.bioinf.gui.misc.ChunkyListModel</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+delegate</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Vector.html">Vector</A> <B>delegate</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.optionable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.optionable.OptionableJFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">uk.ac.man.bioinf.gui.optionable.OptionableJFrame</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+optionableName</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>optionableName</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+optionHandler</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>optionHandler</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+sizeSetAsOption</H3>
+<PRE>
+boolean <B>sizeSetAsOption</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+locationSetAsOption</H3>
+<PRE>
+boolean <B>locationSetAsOption</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+haveOptioned</H3>
+<PRE>
+boolean <B>haveOptioned</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+optionableName</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>optionableName</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+optionHandler</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>optionHandler</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+locationSetAsOption</H3>
+<PRE>
+boolean <B>locationSetAsOption</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+haveOptioned</H3>
+<PRE>
+boolean <B>haveOptioned</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.util</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.ApplicationFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/ApplicationFrame.html">uk.ac.man.bioinf.gui.util.ApplicationFrame</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+ra</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A> <B>ra</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+appName</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>appName</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+mb</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A> <B>mb</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+tb</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToolBar.html">JToolBar</A> <B>tb</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+messages</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A> <B>messages</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+menuMapping</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>menuMapping</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+menuItemLocation</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>menuItemLocation</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+menuItemMapping</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>menuItemMapping</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+buttonMapping</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>buttonMapping</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+contentPane</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>contentPane</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+contents</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>contents</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.TripletPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/TripletPanel.html">uk.ac.man.bioinf.gui.util.TripletPanel</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+leftRightSplit</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">JSplitPane</A> <B>leftRightSplit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+upDownSplit</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">JSplitPane</A> <B>upDownSplit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+mainWindow</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>mainWindow</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+topLeft</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>topLeft</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+bottomLeft</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>bottomLeft</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+tlt</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>tlt</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+blt</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>blt</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+rht</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>rht</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+tlp</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>tlp</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+blp</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>blp</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+rhp</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>rhp</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.util.forms</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.DecimalField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/DecimalField.html">uk.ac.man.bioinf.gui.util.forms.DecimalField</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+format</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> <B>format</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.FormattedDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html">uk.ac.man.bioinf.gui.util.forms.FormattedDocument</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+format</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/Format.html">Format</A> <B>format</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.IntegerField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.html">uk.ac.man.bioinf.gui.util.forms.IntegerField</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+toolkit</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Toolkit.html">Toolkit</A> <B>toolkit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+integerFormatter</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> <B>integerFormatter</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html">uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.ValidatedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html">uk.ac.man.bioinf.gui.util.forms.ValidatedForm</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+labels</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>labels</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+fields</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>fields</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+modifiers</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>modifiers</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+changes</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>changes</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+c</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/GridBagConstraints.html">GridBagConstraints</A> <B>c</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+gridbag</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/GridBagLayout.html">GridBagLayout</A> <B>gridbag</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+currentRow</H3>
+<PRE>
+int <B>currentRow</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+myDocumentListener</H3>
+<PRE>
+ValidatedForm.MyDocumentListener <B>myDocumentListener</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.WholeNumberField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">uk.ac.man.bioinf.gui.util.forms.WholeNumberField</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+toolkit</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Toolkit.html">Toolkit</A> <B>toolkit</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+integerFormatter</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> <B>integerFormatter</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html">uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.viewer</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html">uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+titleLabel</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A> <B>titleLabel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+currentSequence</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>currentSequence</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html">uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+green</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/border/Border.html">Border</A> <B>green</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+red</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/border/Border.html">Border</A> <B>red</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+black</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/border/Border.html">Border</A> <B>black</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+empty</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/border/Border.html">Border</A> <B>empty</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html">uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+itemListener</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A> <B>itemListener</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+prototypicalCellHeight</H3>
+<PRE>
+int <B>prototypicalCellHeight</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+buttonMap</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Map.html">Map</A> <B>buttonMap</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+colorMap</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Map.html">Map</A> <B>colorMap</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+msa</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>msa</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+preferredSize</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>preferredSize</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.JAlignmentRuler"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">uk.ac.man.bioinf.gui.viewer.JAlignmentRuler</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+widthPerBase</H3>
+<PRE>
+int <B>widthPerBase</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+preferredHeight</H3>
+<PRE>
+int <B>preferredHeight</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+seq</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>seq</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.JAlignmentViewer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">uk.ac.man.bioinf.gui.viewer.JAlignmentViewer</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+alignment</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>alignment</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+prototypicalCellSize</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>prototypicalCellSize</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+renderer</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A> <B>renderer</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+fastRenderer</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A> <B>fastRenderer</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+selectionRenderer</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A> <B>selectionRenderer</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+cursor</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A> <B>cursor</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+viewerUI</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A> <B>viewerUI</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+selectionModel</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> <B>selectionModel</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+colorMap</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>colorMap</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+preferredSize</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>preferredSize</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+cacheRect</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>cacheRect</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+readonly</H3>
+<PRE>
+boolean <B>readonly</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+viewerRect</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>viewerRect</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+previousSelection</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>previousSelection</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.JChangedScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html">uk.ac.man.bioinf.gui.viewer.JChangedScrollPane</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.JLayableScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html">uk.ac.man.bioinf.gui.viewer.JLayableScrollPane</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html">uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.ReadonlyException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">uk.ac.man.bioinf.gui.viewer.ReadonlyException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+viewer</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>viewer</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.viewer.event</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+rectangle</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>rectangle</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+isAdjusting</H3>
+<PRE>
+boolean <B>isAdjusting</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.gui.viewer.test</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html">uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+blinkOn</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>blinkOn</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+blinkOff</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>blinkOff</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+viewer</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>viewer</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html">uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.gui.viewer.test.SliderExample"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/gui/viewer/test/SliderExample.html">uk.ac.man.bioinf.gui.viewer.test.SliderExample</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.io</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.io.InvalidSequenceTypeParserException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">uk.ac.man.bioinf.io.InvalidSequenceTypeParserException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+expectedSequenceType</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>expectedSequenceType</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.io.ParserException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/io/ParserException.html">uk.ac.man.bioinf.io.ParserException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+position</H3>
+<PRE>
+int <B>position</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+sequence</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>sequence</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+identifier</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>identifier</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.io.SequenceWriterException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/io/SequenceWriterException.html">uk.ac.man.bioinf.io.SequenceWriterException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.io.UnknownElementException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/io/UnknownElementException.html">uk.ac.man.bioinf.io.UnknownElementException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.module</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.module.ModuleException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/module/ModuleException.html">uk.ac.man.bioinf.module.ModuleException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+id</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>id</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+throwable</H3>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> <B>throwable</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.module.NoSuchRequiredModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/module/NoSuchRequiredModule.html">uk.ac.man.bioinf.module.NoSuchRequiredModule</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+ident</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>ident</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.sequence</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.InvalidSequenceTypeException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">uk.ac.man.bioinf.sequence.InvalidSequenceTypeException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.NoSuchSequenceElementException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">uk.ac.man.bioinf.sequence.NoSuchSequenceElementException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.SequenceException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/SequenceException.html">uk.ac.man.bioinf.sequence.SequenceException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.sequence.alignment</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+source</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>source</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+index</H3>
+<PRE>
+int <B>index</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.sequence.alignment.event</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+start</H3>
+<PRE>
+int <B>start</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+end</H3>
+<PRE>
+int <B>end</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+type</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>type</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+event</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> <B>event</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.sequence.event</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.event.SequenceEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">uk.ac.man.bioinf.sequence.event.SequenceEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+start</H3>
+<PRE>
+int <B>start</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+length</H3>
+<PRE>
+int <B>length</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<H3>
+type</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>type</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.event.SequenceVetoException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">uk.ac.man.bioinf.sequence.event.SequenceVetoException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="serializedForm"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Serialized Fields</B></FONT></TD>
+</TR>
+</TABLE>
+
+<H3>
+event</H3>
+<PRE>
+<A HREF="uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> <B>event</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.sequence.complex</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html">uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.complex.NoSuchModificationException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html">uk.ac.man.bioinf.sequence.complex.NoSuchModificationException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.sequence.identifier</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html">uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR SIZE="4" NOSHADE>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD ALIGN="center"><FONT SIZE="+2">
+<B>Package</B> <B>uk.ac.man.bioinf.util</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+<A NAME="uk.ac.man.bioinf.util.ChangeableEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class <A HREF="uk/ac/man/bioinf/util/ChangeableEvent.html">uk.ac.man.bioinf.util.ChangeableEvent</A> implements Serializable</B></FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Package</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="serialized-form.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/stylesheet.css b/doc/javadoc/stylesheet.css
new file mode 100644
index 0000000..b62ecb5
--- /dev/null
+++ b/doc/javadoc/stylesheet.css
@@ -0,0 +1,29 @@
+/* Javadoc style sheet */
+
+/* Define colors, fonts and other style attributes here to override the defaults */
+
+/* Page background color */
+body { background-color: #FFFFFF }
+
+/* Table colors */
+.TableHeadingColor { background: #CCCCFF } /* Dark mauve */
+.TableSubHeadingColor { background: #EEEEFF } /* Light mauve */
+.TableRowColor { background: #FFFFFF } /* White */
+
+/* Font used in left-hand frame lists */
+.FrameTitleFont { font-size: 10pts; font-family: Helvetica, Arial, san-serif }
+.FrameHeadingFont { font-size: 10pts; font-family: Helvetica, Arial, san-serif }
+.FrameItemFont { font-size: 10pts; font-family: Helvetica, Arial, san-serif }
+
+/* Example of smaller, sans-serif font in frames */
+/* .FrameItemFont { font-size: 10pt; font-family: Helvetica, Arial, sans-serif } */
+
+/* Navigation bar fonts and colors */
+.NavBarCell1 { background-color:#EEEEFF;}/* Light mauve */
+.NavBarCell1Rev { background-color:#00008B;}/* Dark Blue */
+.NavBarFont1 { font-family: Arial, Helvetica, sans-serif; color:#000000;}
+.NavBarFont1Rev { font-family: Arial, Helvetica, sans-serif; color:#FFFFFF;}
+
+.NavBarCell2 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF;}
+.NavBarCell3 { font-family: Arial, Helvetica, sans-serif; background-color:#FFFFFF;}
+
diff --git a/doc/javadoc/uk/ac/man/bioinf/Y.html b/doc/javadoc/uk/ac/man/bioinf/Y.html
new file mode 100644
index 0000000..24c6e9b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/Y.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:14 BST 2002 -->
+<TITLE>
+Y
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Y";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Y.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf</FONT>
+<BR>
+Class Y</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.Y</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Y</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Y.java
+
+ Class created entirely for the purpose of being tab
+ completable. Originally I used X.java, which is not buzz word
+ compliant, as I have forgotten about XML. Idiot!
+
+ Created: Mon May 8 21:24:52 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Y.java,v 1.1 2000/05/15 16:19:46 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../uk/ac/man/bioinf/Y.html#Y()">Y</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Y()"><!-- --></A><H3>
+Y</H3>
+<PRE>
+public <B>Y</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Y.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html
new file mode 100644
index 0000000..271e201
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:14 BST 2002 -->
+<TITLE>
+ConsensusCalculator
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ConsensusCalculator";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusCalculator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.consensus</FONT>
+<BR>
+Interface ConsensusCalculator</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html">PercentageIDConsensus</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ConsensusCalculator</B></DL>
+
+<P>
+ConsensusCalculator.java
+
+
+ Created: Thu Jun 15 15:11:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ConsensusCalculator.java,v 1.6 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getCalculatorName()">getCalculatorName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getCurrentConsensus()">getCurrentConsensus</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getSequenceAlignment()">getSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSequenceAlignment()"><!-- --></A><H3>
+getSequenceAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSequenceAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentConsensus()"><!-- --></A><H3>
+getCurrentConsensus</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getCurrentConsensus</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCalculatorName()"><!-- --></A><H3>
+getCalculatorName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getCalculatorName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusCalculator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html
new file mode 100644
index 0000000..1aa1279
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:14 BST 2002 -->
+<TITLE>
+ConsensusIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ConsensusIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.consensus</FONT>
+<BR>
+Class ConsensusIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ConsensusIdentifier</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></DL>
+
+<P>
+ConsensusIdentifier.java
+
+
+ Created: Mon Oct 16 15:40:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ConsensusIdentifier.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html#ConsensusIdentifier(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">ConsensusIdentifier</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html#ConsensusIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">ConsensusIdentifier</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Gets a human readable title for the Sequence</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#getSource()">getSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ConsensusIdentifier(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+ConsensusIdentifier</H3>
+<PRE>
+public <B>ConsensusIdentifier</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ConsensusIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+ConsensusIdentifier</H3>
+<PRE>
+public <B>ConsensusIdentifier</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></B></DD>
+<DD>Gets a human readable title for the Sequence
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html
new file mode 100644
index 0000000..7cab44a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:14 BST 2002 -->
+<TITLE>
+ConsensusSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ConsensusSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.consensus</FONT>
+<BR>
+Interface ConsensusSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventP [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ConsensusSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></DL>
+
+<P>
+ConsensusSequence.java
+
+
+ Created: Thu Jun 15 15:32:13 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ConsensusSequence.java,v 1.4 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#getConsensusCalculator()">getConsensusCalculator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">setConsensusCalculator</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calc)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.GappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(i [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/S [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+setConsensusCalculator</H3>
+<PRE>
+public void <B>setConsensusCalculator</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calc)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusCalculator()"><!-- --></A><H3>
+getConsensusCalculator</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> <B>getConsensusCalculator</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html
new file mode 100644
index 0000000..d2004d9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html
@@ -0,0 +1,849 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:14 BST 2002 -->
+<TITLE>
+DefaultConsensusSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultConsensusSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultConsensusSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.consensus</FONT>
+<BR>
+Class DefaultConsensusSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../ [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html">ThreadedConsensusSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultConsensusSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListen [...]
+
+<P>
+DefaultConsensusSequence.java
+
+
+ Created: Thu Jun 15 17:00:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultConsensusSequence.java,v 1.8 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#DefaultConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">DefaultConsensusSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#calcConsensus()">calcConsensus</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#deleteGapAtQuietly(int)">deleteGapAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#fireChangeEvent()">fireChangeEvent</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getConsensusCalculator()">getConsensusCalculator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedElementAt(int)">getGappedElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedLength()">getGappedLength</A></B>()</CODE>
+
+<BR>
+ Returns the gapped length of this sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></B>(int index)</CODE>
+
+<BR>
+ Translate between the gapped index, and the ungapped index</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></B>(int start,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></B>(int index)</CODE>
+
+<BR>
+ Translate between the gapped position and the ungapped
+ position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#insertGapAtQuietly(int)">insertGapAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#installAlignmentListeners(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">installAlignmentListeners</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> cons)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#installVetoListeners()">installVetoListeners</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">setConsensusCalculator</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#uninstallAlignmentListners(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">uninstallAlignmentListners</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> cons)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#validate()">validate</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRange(int)">checkGappedRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRangeForInsert(int)">checkGappedRangeForInsert</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Abs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequenc [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.GappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSeque [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+DefaultConsensusSequence</H3>
+<PRE>
+public <B>DefaultConsensusSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="installVetoListeners()"><!-- --></A><H3>
+installVetoListeners</H3>
+<PRE>
+protected void <B>installVetoListeners</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="installAlignmentListeners(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+installAlignmentListeners</H3>
+<PRE>
+protected void <B>installAlignmentListeners</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> cons)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="uninstallAlignmentListners(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+uninstallAlignmentListners</H3>
+<PRE>
+protected void <B>uninstallAlignmentListners</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> cons)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="validate()"><!-- --></A><H3>
+validate</H3>
+<PRE>
+protected void <B>validate</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireChangeEvent()"><!-- --></A><H3>
+fireChangeEvent</H3>
+<PRE>
+protected void <B>fireChangeEvent</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calcConsensus()"><!-- --></A><H3>
+calcConsensus</H3>
+<PRE>
+protected void <B>calcConsensus</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAt(int)"><!-- --></A><H3>
+getGappedElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getGappedElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedLength()"><!-- --></A><H3>
+getGappedLength</H3>
+<PRE>
+public int <B>getGappedLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Returns the gapped length of this sequence. That is the length of
+ the sequence including its gaps. Conversely this means that the
+ getLength method of the Sequence interface returns the length of
+ the sequence ignoring the gaps.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedLength()">getGappedLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedPositionOf(int)"><!-- --></A><H3>
+getGappedPositionOf</H3>
+<PRE>
+public int <B>getGappedPositionOf</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped index, and the ungapped index
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the ungapped position
+<DT><B>Returns:</B><DD>the gapped position of the equivalent element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsElements()"><!-- --></A><H3>
+getGappedSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getGappedSequenceAsElements</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSubSequence(int, int)"><!-- --></A><H3>
+getGappedSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getGappedSubSequence</B>(int start,
+ int length)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUngappedPositionOf(int)"><!-- --></A><H3>
+getUngappedPositionOf</H3>
+<PRE>
+public int <B>getUngappedPositionOf</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped position and the ungapped
+ position. I havent quite decided what to do at the moment if the
+ index refers to a gap. One idea is to throw a
+ NoSuchSequenceElementException which makes a certain amount of
+ sense but isnt really that useful. Perhaps a better idea is to
+ run -(insertion-point) where the insertion point is the nearest
+ element before the current requested position which is not a
+ gap. That way a value less than 0 would indicate a gap and would
+ also return a useful value
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+setConsensusCalculator</H3>
+<PRE>
+public void <B>setConsensusCalculator</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#setConsensusCalculator(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">setConsensusCalculator</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusCalculator()"><!-- --></A><H3>
+getConsensusCalculator</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> <B>getConsensusCalculator</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#getConsensusCalculator()">getConsensusCalculator</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAtQuietly(int)"><!-- --></A><H3>
+deleteGapAtQuietly</H3>
+<PRE>
+public void <B>deleteGapAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAtQuietly(int)">deleteGapAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAtQuietly(int)"><!-- --></A><H3>
+insertGapAtQuietly</H3>
+<PRE>
+public void <B>insertGapAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAtQuietly(int)">insertGapAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#destroy()">destroy</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultConsensusSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html
new file mode 100644
index 0000000..c6d585f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html
@@ -0,0 +1,336 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+PercentageIDConsensus
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PercentageIDConsensus";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDConsensus.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.consensus</FONT>
+<BR>
+Class PercentageIDConsensus</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PercentageIDConsensus</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></DL>
+
+<P>
+PercentageIDConsensus.java
+
+ Calculates a consensus sequence based simply on which element is
+ most frequent at that row. If there are several possibilities it
+ just takes which ever one came first.
+
+ Created: Thu Jun 15 18:06:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PercentageIDConsensus.java,v 1.10 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#PercentageIDConsensus(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator)">PercentageIDConsensus</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> calc)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#getCalculatorName()">getCalculatorName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#getCurrentConsensus()">getCurrentConsensus</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html#getSequenceAlignment()">getSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PercentageIDConsensus(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator)"><!-- --></A><H3>
+PercentageIDConsensus</H3>
+<PRE>
+public <B>PercentageIDConsensus</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> calc)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getCurrentConsensus()"><!-- --></A><H3>
+getCurrentConsensus</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getCurrentConsensus</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getCurrentConsensus()">getCurrentConsensus</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCalculatorName()"><!-- --></A><H3>
+getCalculatorName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getCalculatorName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getCalculatorName()">getCalculatorName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAlignment()"><!-- --></A><H3>
+getSequenceAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSequenceAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html#getSequenceAlignment()">getSequenceAlignment</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDConsensus.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html
new file mode 100644
index 0000000..a3b63a9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html
@@ -0,0 +1,410 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+ThreadedConsensusSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ThreadedConsensusSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedConsensusSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.consensus</FONT>
+<BR>
+Class ThreadedConsensusSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ThreadedConsensusSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A></DL>
+
+<P>
+ThreadedConsensusSequence.java
+
+ This class calls the calculation out of the event thread, so that
+ background analysis is made more easily. To use this class you have
+ to provide it with a thread that it can use for the
+ calculation. You can do this either on a per instance basis, or by
+ setting a static default. You have to do one of the other though!
+
+ Created: Tue Nov 7 18:36:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ThreadedConsensusSequence.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#ThreadedConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">ThreadedConsensusSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#ThreadedConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator, uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)">ThreadedConsensusSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> queue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#getDefaultInvokerInternalQueue()">getDefaultInvokerInternalQueue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#setDefaultInvokerInternalQueue(uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)">setDefaultInvokerInternalQueue</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> queue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html#validate()">validate</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#calcConsensus()">calcConsensus</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccu [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRange(int)">checkGappedRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRangeForInsert(int)">checkGappedRangeForInsert</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Abs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequenc [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.GappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSeque [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ThreadedConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+ThreadedConsensusSequence</H3>
+<PRE>
+public <B>ThreadedConsensusSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ThreadedConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator, uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)"><!-- --></A><H3>
+ThreadedConsensusSequence</H3>
+<PRE>
+public <B>ThreadedConsensusSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calculator,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> queue)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="validate()"><!-- --></A><H3>
+validate</H3>
+<PRE>
+protected void <B>validate</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#validate()">validate</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html#destroy()">destroy</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html#destroy()">destroy</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bi [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDefaultInvokerInternalQueue(uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)"><!-- --></A><H3>
+setDefaultInvokerInternalQueue</H3>
+<PRE>
+public static void <B>setDefaultInvokerInternalQueue</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> queue)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDefaultInvokerInternalQueue()"><!-- --></A><H3>
+getDefaultInvokerInternalQueue</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> <B>getDefaultInvokerInternalQueue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedConsensusSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-frame.html
new file mode 100644
index 0000000..cebc857
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-frame.html
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.consensus()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.consensus()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.analysis.consensus</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ConsensusCalculator.html" TARGET="classFrame"><I>ConsensusCalculator</I></A>
+<BR>
+<A HREF="ConsensusSequence.html" TARGET="classFrame"><I>ConsensusSequence</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ConsensusIdentifier.html" TARGET="classFrame">ConsensusIdentifier</A>
+<BR>
+<A HREF="DefaultConsensusSequence.html" TARGET="classFrame">DefaultConsensusSequence</A>
+<BR>
+<A HREF="PercentageIDConsensus.html" TARGET="classFrame">PercentageIDConsensus</A>
+<BR>
+<A HREF="ThreadedConsensusSequence.html" TARGET="classFrame">ThreadedConsensusSequence</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-summary.html
new file mode 100644
index 0000000..18c8db5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-summary.html
@@ -0,0 +1,182 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.consensus()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.consensus()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.analysis.consensus
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ConsensusCalculator.html"><I>ConsensusCalculator</I></A></B></TD>
+<TD>ConsensusCalculator.java
+
+
+ Created: Thu Jun 15 15:11:33 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ConsensusSequence.html"><I>ConsensusSequence</I></A></B></TD>
+<TD>ConsensusSequence.java
+
+
+ Created: Thu Jun 15 15:32:13 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ConsensusIdentifier.html">ConsensusIdentifier</A></B></TD>
+<TD>ConsensusIdentifier.java
+
+
+ Created: Mon Oct 16 15:40:30 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultConsensusSequence.html">DefaultConsensusSequence</A></B></TD>
+<TD>DefaultConsensusSequence.java
+
+
+ Created: Thu Jun 15 17:00:04 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PercentageIDConsensus.html">PercentageIDConsensus</A></B></TD>
+<TD>PercentageIDConsensus.java
+
+ Calculates a consensus sequence based simply on which element is
+ most frequent at that row.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ThreadedConsensusSequence.html">ThreadedConsensusSequence</A></B></TD>
+<TD>ThreadedConsensusSequence.java
+
+ This class calls the calculation out of the event thread, so that
+ background analysis is made more easily.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-tree.html
new file mode 100644
index 0000000..07da31c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/consensus/package-tree.html
@@ -0,0 +1,169 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.consensus Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.consensus Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.analysis.consensus
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html"><B>AbstractIdentifier</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html"><B>ConsensusIdentifier</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>AbstractSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>AbstractMutableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html"><B>AbstractGappedSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html"><B>DefaultConsensusSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">Consensus [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.html"><B>ThreadedConsensusSequence</B></A></UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.html"><B>PercentageIDConsensus</B></A> (implements uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A>)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html"><B>ConsensusCalculator</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>Sequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>ConsensusSequence</B></A></UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>SequenceEventProvider</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.analysis.consensus.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html"><B>ConsensusSequence</B></A></UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html
new file mode 100644
index 0000000..566e132
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html
@@ -0,0 +1,383 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+PercentageIDCalculator
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PercentageIDCalculator";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDCalculator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.misc</FONT>
+<BR>
+Class PercentageIDCalculator</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PercentageIDCalculator</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></DL>
+
+<P>
+PercentageIDCalculator.java
+
+ This class performs a variance calculation on the given sequence
+ alignment. The calculation is done by calling the
+ calculateAlignment method, and the results got from the
+ getVariance, and getConsensus methods. Both calculations are done
+ by a simple Percentage ID calculation.
+
+ Created: Fri Jun 16 18:38:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PercentageIDCalculator.java,v 1.6 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#PercentageIDCalculator(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">PercentageIDCalculator</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getAlignment()">getAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getCheckSum()">getCheckSum</A></B>()</CODE>
+
+<BR>
+ Returns a checksum value.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getConsensus()">getConsensus</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> double[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html#getVariance()">getVariance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PercentageIDCalculator(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+PercentageIDCalculator</H3>
+<PRE>
+public <B>PercentageIDCalculator</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCheckSum()"><!-- --></A><H3>
+getCheckSum</H3>
+<PRE>
+public int <B>getCheckSum</B>()</PRE>
+<DL>
+<DD>Returns a checksum value. If this value has changed there
+ consensus sequence may well have changed.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>a value of type 'int'</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVariance()"><!-- --></A><H3>
+getVariance</H3>
+<PRE>
+public double[] <B>getVariance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensus()"><!-- --></A><H3>
+getConsensus</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getConsensus</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignment()"><!-- --></A><H3>
+getAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDCalculator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html
new file mode 100644
index 0000000..9f71507
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html
@@ -0,0 +1,271 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+PercentageIDCalculatorManager
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PercentageIDCalculatorManager";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDCalculatorManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.misc</FONT>
+<BR>
+Class PercentageIDCalculatorManager</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>PercentageIDCalculatorManager</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+PercentageIDCalculatorManager.java
+
+
+ Created: Tue Nov 7 17:59:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PercentageIDCalculatorManager.java,v 1.2 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html#PercentageIDCalculatorManager()">PercentageIDCalculatorManager</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html#getCalculator(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getCalculator</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html#getDefaultInstance()">getDefaultInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PercentageIDCalculatorManager()"><!-- --></A><H3>
+PercentageIDCalculatorManager</H3>
+<PRE>
+public <B>PercentageIDCalculatorManager</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getCalculator(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+getCalculator</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> <B>getCalculator</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDefaultInstance()"><!-- --></A><H3>
+getDefaultInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A> <B>getDefaultInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDCalculatorManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-frame.html
new file mode 100644
index 0000000..fa5b053
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.misc()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.misc()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.analysis.misc</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="PercentageIDCalculator.html" TARGET="classFrame">PercentageIDCalculator</A>
+<BR>
+<A HREF="PercentageIDCalculatorManager.html" TARGET="classFrame">PercentageIDCalculatorManager</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-summary.html
new file mode 100644
index 0000000..80c5bd9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-summary.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.misc()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.misc()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.analysis.misc
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PercentageIDCalculator.html">PercentageIDCalculator</A></B></TD>
+<TD>PercentageIDCalculator.java
+
+ This class performs a variance calculation on the given sequence
+ alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PercentageIDCalculatorManager.html">PercentageIDCalculatorManager</A></B></TD>
+<TD>PercentageIDCalculatorManager.java
+
+
+ Created: Tue Nov 7 17:59:02 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-tree.html
new file mode 100644
index 0000000..ff728b9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/misc/package-tree.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.misc Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.misc Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.analysis.misc
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.misc.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html"><B>PercentageIDCalculator</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.misc.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.html"><B>PercentageIDCalculatorManager</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html
new file mode 100644
index 0000000..fa6cabc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html
@@ -0,0 +1,311 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+GappedSequenceCharacterIterator
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappedSequenceCharacterIterator";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceCharacterIterator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.regexp</FONT>
+<BR>
+Class GappedSequenceCharacterIterator</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>GappedSequenceCharacterIterator</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+GappedSequenceCharacterIterator.java
+
+
+ Created: Mon Feb 5 14:06:28 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappedSequenceCharacterIterator.java,v 1.2 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#GappedSequenceCharacterIterator(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">GappedSequenceCharacterIterator</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#charAt(int)">charAt</A></B>(int at)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#isEnd(int)">isEnd</A></B>(int position)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#substring(int)">substring</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html#substring(int, int)">substring</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GappedSequenceCharacterIterator(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+GappedSequenceCharacterIterator</H3>
+<PRE>
+public <B>GappedSequenceCharacterIterator</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="charAt(int)"><!-- --></A><H3>
+charAt</H3>
+<PRE>
+public char <B>charAt</B>(int at)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isEnd(int)"><!-- --></A><H3>
+isEnd</H3>
+<PRE>
+public boolean <B>isEnd</B>(int position)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="substring(int)"><!-- --></A><H3>
+substring</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>substring</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="substring(int, int)"><!-- --></A><H3>
+substring</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>substring</B>(int index,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceCharacterIterator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html
new file mode 100644
index 0000000..88da86f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html
@@ -0,0 +1,312 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+SequenceCharacterIterator
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceCharacterIterator";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceCharacterIterator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.analysis.regexp</FONT>
+<BR>
+Class SequenceCharacterIterator</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceCharacterIterator</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceCharacterIterator.java
+
+ This class provides the link between the sequence package and
+ jakarta regexp package. This class can be used as a wrapper for
+ Sequences.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceCharacterIterator.java,v 1.2 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html"><CODE>Created: Mon Feb 5 13:53:45 2001</CODE></A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#SequenceCharacterIterator(uk.ac.man.bioinf.sequence.Sequence)">SequenceCharacterIterator</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#charAt(int)">charAt</A></B>(int at)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#isEnd(int)">isEnd</A></B>(int position)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#substring(int)">substring</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html#substring(int, int)">substring</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceCharacterIterator(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+SequenceCharacterIterator</H3>
+<PRE>
+public <B>SequenceCharacterIterator</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="charAt(int)"><!-- --></A><H3>
+charAt</H3>
+<PRE>
+public char <B>charAt</B>(int at)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isEnd(int)"><!-- --></A><H3>
+isEnd</H3>
+<PRE>
+public boolean <B>isEnd</B>(int position)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="substring(int)"><!-- --></A><H3>
+substring</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>substring</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="substring(int, int)"><!-- --></A><H3>
+substring</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>substring</B>(int index,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceCharacterIterator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-frame.html
new file mode 100644
index 0000000..24be8ee
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.regexp()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.regexp()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.analysis.regexp</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="GappedSequenceCharacterIterator.html" TARGET="classFrame">GappedSequenceCharacterIterator</A>
+<BR>
+<A HREF="SequenceCharacterIterator.html" TARGET="classFrame">SequenceCharacterIterator</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-summary.html
new file mode 100644
index 0000000..589ebb2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-summary.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.regexp()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.regexp()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.analysis.regexp
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappedSequenceCharacterIterator.html">GappedSequenceCharacterIterator</A></B></TD>
+<TD>GappedSequenceCharacterIterator.java
+
+
+ Created: Mon Feb 5 14:06:28 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceCharacterIterator.html">SequenceCharacterIterator</A></B></TD>
+<TD>SequenceCharacterIterator.java
+
+ This class provides the link between the sequence package and
+ jakarta regexp package.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-tree.html
new file mode 100644
index 0000000..fcb8db3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/analysis/regexp/package-tree.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.analysis.regexp Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.analysis.regexp Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.analysis.regexp
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.analysis.regexp.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.html"><B>GappedSequenceCharacterIterator</B></A><LI TYPE="circle">class uk.ac.man.bioinf.analysis.regexp.<A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.html"><B>SequenceCharacterIterator</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/Cinema.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/Cinema.html
new file mode 100644
index 0000000..ebeb792
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/Cinema.html
@@ -0,0 +1,318 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:16 BST 2002 -->
+<TITLE>
+Cinema
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Cinema";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Cinema.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class Cinema</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.Cinema</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Cinema</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Cinema.java
+
+
+ Created: Fri May 26 22:04:20 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Cinema.java,v 1.15 2001/05/04 12:30:32 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html#Cinema()">Cinema</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html#getCommandLineArguments()">getCommandLineArguments</A></B>()</CODE>
+
+<BR>
+ Returns the arguments supplied to Cinema on the command line, and
+ stored in the 'main' function.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html#getSharedModuleInstance(uk.ac.man.bioinf.module.ModuleIdentifier)">getSharedModuleInstance</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html#startCinemaInstance()">startCinemaInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Cinema()"><!-- --></A><H3>
+Cinema</H3>
+<PRE>
+public <B>Cinema</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCommandLineArguments()"><!-- --></A><H3>
+getCommandLineArguments</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] <B>getCommandLineArguments</B>()</PRE>
+<DL>
+<DD>Returns the arguments supplied to Cinema on the command line, and
+ stored in the 'main' function.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the arguments</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSharedModuleInstance(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getSharedModuleInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getSharedModuleInstance</B>(<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="startCinemaInstance()"><!-- --></A><H3>
+startCinemaInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A> <B>startCinemaInstance</B>()
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Cinema.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaBoot.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaBoot.html
new file mode 100644
index 0000000..dfbdcbd
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaBoot.html
@@ -0,0 +1,391 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:17 BST 2002 -->
+<TITLE>
+CinemaBoot
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaBoot";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaBoot.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaBoot</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">uk.ac.man.bioinf.apps.xml.XMLBootModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaBoot</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html">CinemaShared</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaBoot</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></DL>
+
+<P>
+CinemaBoot.java
+
+
+ Created: Mon May 29 17:58:12 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaBoot.java,v 1.8 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#CinemaBoot()">CinemaBoot</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#fetchMainBootName()">fetchMainBootName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#fetchModuleSystemIdentifier()">fetchModuleSystemIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#getXMLParserClass()">getXMLParserClass</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#resolveXMLLoadName(java.lang.String)">resolveXMLLoadName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> loadName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#characters(java.lang.String)">characters</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#classEnd()">classEnd</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#configStart(org.xml.sax.Attributes)">configStart</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#enumerationEnd()">enumerationEnd</A>, <A HREF="../../../../../../uk/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#fi [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaBoot()"><!-- --></A><H3>
+CinemaBoot</H3>
+<PRE>
+public <B>CinemaBoot</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fetchMainBootName()"><!-- --></A><H3>
+fetchMainBootName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchMainBootName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#fetchMainBootName()">fetchMainBootName</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fetchModuleSystemIdentifier()"><!-- --></A><H3>
+fetchModuleSystemIdentifier</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchModuleSystemIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#fetchModuleSystemIdentifier()">fetchModuleSystemIdentifier</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveXMLLoadName(java.lang.String)"><!-- --></A><H3>
+resolveXMLLoadName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>resolveXMLLoadName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> loadName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#resolveXMLLoadName(java.lang.String)">resolveXMLLoadName</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getXMLParserClass()"><!-- --></A><H3>
+getXMLParserClass</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getXMLParserClass</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#getXMLParserClass()">getXMLParserClass</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaBoot.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html
new file mode 100644
index 0000000..8d525d3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:17 BST 2002 -->
+<TITLE>
+CinemaBootIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaBootIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaBootIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaBootIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaBootIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaBootIdentifier</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaBootIdentifier.java
+
+
+ Created: Mon May 29 18:09:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaBootIdentifier.java,v 1.4 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html#CINEMA_BOOT">CINEMA_BOOT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html#CINEMA_SHARED">CINEMA_SHARED</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdent [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_BOOT"><!-- --></A><H3>
+CINEMA_BOOT</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A> <B>CINEMA_BOOT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_SHARED"><!-- --></A><H3>
+CINEMA_SHARED</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A> <B>CINEMA_SHARED</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaBootIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html
new file mode 100644
index 0000000..5e72236
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html
@@ -0,0 +1,518 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:17 BST 2002 -->
+<TITLE>
+CinemaGuiModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGuiModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGuiModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaGuiModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensu [...]
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>CinemaGuiModule</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaGuiModule.java
+
+
+ Created: Fri May 26 21:04:15 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGuiModule.java,v 1.8 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#CinemaGuiModule()">CinemaGuiModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ The method called, from an external source, to remove this module
+ and prepare it for garbage collection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRowHeaders()">getRowHeaders</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRuler()">getRuler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRulerPanel()">getRulerPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getScrollPane()">getScrollPane</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getStatusBar()">getStatusBar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getViewer()">getViewer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#setFrameTitle(java.lang.String)">setFrameTitle</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.lang.Stri [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html# [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaGuiModule()"><!-- --></A><H3>
+CinemaGuiModule</H3>
+<PRE>
+public <B>CinemaGuiModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#destroy()">destroy</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFrame()"><!-- --></A><H3>
+getFrame</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> <B>getFrame</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setFrameTitle(java.lang.String)"><!-- --></A><H3>
+setFrameTitle</H3>
+<PRE>
+public void <B>setFrameTitle</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRowHeaders()"><!-- --></A><H3>
+getRowHeaders</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A> <B>getRowHeaders</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getJMenuBar()"><!-- --></A><H3>
+getJMenuBar</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A> <B>getJMenuBar</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollPane()"><!-- --></A><H3>
+getScrollPane</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>getScrollPane</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRulerPanel()"><!-- --></A><H3>
+getRulerPanel</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>getRulerPanel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getViewer()"><!-- --></A><H3>
+getViewer</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>getViewer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRuler()"><!-- --></A><H3>
+getRuler</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A> <B>getRuler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getStatusBar()"><!-- --></A><H3>
+getStatusBar</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A> <B>getStatusBar</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignmentFrame()"><!-- --></A><H3>
+getAlignmentFrame</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> <B>getAlignmentFrame</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGuiModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaModule.html
new file mode 100644
index 0000000..728c632
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaModule.html
@@ -0,0 +1,753 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:18 BST 2002 -->
+<TITLE>
+CinemaModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaModule</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html">CinemaCommandLineParser</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>, <A HR [...]
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>CinemaModule</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DL>
+
+<P>
+CinemaModule.java
+
+ Most modules for Cinema should extend this interface. It provides
+ access to most of the functions of Cinema without being to tied to
+ the main GUI components, which should insulate these modules from
+ any changes which are made to it.
+
+ I intend to include a few other methods here. I think that the
+ CinemaModule should provide access to listeners for the cursor for
+ instance, as this is a concept relatively divorced from that of the
+ GUI.
+
+ Created: Fri May 26 16:04:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaModule.java,v 1.7 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#CinemaModule()">CinemaModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Add a listener specifically interested in events connected with the MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a listener interested in vetoing multiple sequence alignment
+ specific events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">clearSequenceTitleColor</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ The method called, from an external source, to remove this module
+ and prepare it for garbage collection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#fireCinemaPropertyChange(java.lang.String, java.lang.Object, java.lang.Object)">fireCinemaPropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> old,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> newV)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getAlignmentSelectionModel()">getAlignmentSelectionModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getColorMap()">getColorMap</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getSequenceAlignment()">getSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">removeCinemaPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">removeCinemaPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#sendStatusMessage(java.lang.String)">sendStatusMessage</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)">setAlignmentSelectionModel</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> model)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)">setColorMap</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> map)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq)</CODE>
+
+<BR>
+ Set the Sequence Alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)">setSequenceTitleColor</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> colour)</CODE>
+
+<BR>
+ This sets the colour that is used to display the sequence
+ title.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html# [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaModule()"><!-- --></A><H3>
+CinemaModule</H3>
+<PRE>
+public <B>CinemaModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSequenceAlignment()"><!-- --></A><H3>
+getSequenceAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSequenceAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setSequenceAlignment</H3>
+<PRE>
+public void <B>setSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq)</PRE>
+<DL>
+<DD>Set the Sequence Alignment. Signals a property change event.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMap()"><!-- --></A><H3>
+getColorMap</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getColorMap</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)"><!-- --></A><H3>
+setColorMap</H3>
+<PRE>
+public void <B>setColorMap</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> map)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignmentSelectionModel()"><!-- --></A><H3>
+getAlignmentSelectionModel</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> <B>getAlignmentSelectionModel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)"><!-- --></A><H3>
+setAlignmentSelectionModel</H3>
+<PRE>
+public void <B>setAlignmentSelectionModel</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> model)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)"><!-- --></A><H3>
+setSequenceTitleColor</H3>
+<PRE>
+public void <B>setSequenceTitleColor</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> colour)</PRE>
+<DL>
+<DD>This sets the colour that is used to display the sequence
+ title. NOT the colour of the elements! This is usually done to
+ display some linkage between sequences of the same colour.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - <DD><CODE>colour</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+clearSequenceTitleColor</H3>
+<PRE>
+public void <B>clearSequenceTitleColor</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="sendStatusMessage(java.lang.String)"><!-- --></A><H3>
+sendStatusMessage</H3>
+<PRE>
+public void <B>sendStatusMessage</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireCinemaPropertyChange(java.lang.String, java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+fireCinemaPropertyChange</H3>
+<PRE>
+public void <B>fireCinemaPropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> old,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> newV)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)"><!-- --></A><H3>
+addCinemaPropertyChangeListener</H3>
+<PRE>
+public void <B>addCinemaPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeCinemaPropertyChangeListener(java.beans.PropertyChangeListener)"><!-- --></A><H3>
+removeCinemaPropertyChangeListener</H3>
+<PRE>
+public void <B>removeCinemaPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><!-- --></A><H3>
+addCinemaPropertyChangeListener</H3>
+<PRE>
+public void <B>addCinemaPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><!-- --></A><H3>
+removeCinemaPropertyChangeListener</H3>
+<PRE>
+public void <B>removeCinemaPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Add a listener specifically interested in events connected with the MSA.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Adds a listener interested in vetoing multiple sequence alignment
+ specific events.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a vetoable multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a vetoable multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html
new file mode 100644
index 0000000..1c57143
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html
@@ -0,0 +1,277 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:18 BST 2002 -->
+<TITLE>
+CinemaModuleFactoryInstance
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaModuleFactoryInstance";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaModuleFactoryInstance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaModuleFactoryInstance</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">uk.ac.man.bioinf.module.DefaultModuleFactoryInstance</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaModuleFactoryInstance</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaModuleFactoryInstance</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A></DL>
+
+<P>
+CinemaModuleFactoryInstance.java
+
+ This class adds some reporting functions to the superclass.
+ Created: Wed Aug 2 13:47:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaModuleFactoryInstance.java,v 1.4 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html#CinemaModuleFactoryInstance()">CinemaModuleFactoryInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Loads the module associated with a particular identifier.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.DefaultModuleFactoryInstance"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bio [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaModuleFactoryInstance()"><!-- --></A><H3>
+CinemaModuleFactoryInstance</H3>
+<PRE>
+public <B>CinemaModuleFactoryInstance</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+load</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>load</B>(<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Loads the module associated with a particular identifier. This
+ will include a call to the load method of the module. It should
+ also subsequently check that all requried modules are loaded as
+ well.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></CODE> in cla [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaModuleFactoryInstance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaProperties.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaProperties.html
new file mode 100644
index 0000000..eb862f1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaProperties.html
@@ -0,0 +1,262 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:18 BST 2002 -->
+<TITLE>
+CinemaProperties
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaProperties";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaProperties.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaProperties</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaProperties</B>
+</PRE>
+<HR>
+<DL>
+<DT>public final class <B>CinemaProperties</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></DL>
+
+<P>
+CinemaProperties.java
+
+ This are all of the property names that the CinemaModule signals
+ changes for.
+
+ Created: Fri Jun 2 17:51:43 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaProperties.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html">CinemaProperties</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html#SEQ_ALIGN">SEQ_ALIGN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SEQ_ALIGN"><!-- --></A><H3>
+SEQ_ALIGN</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html">CinemaProperties</A> <B>SEQ_ALIGN</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaProperties.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaShared.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaShared.html
new file mode 100644
index 0000000..ee148df
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaShared.html
@@ -0,0 +1,304 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:18 BST 2002 -->
+<TITLE>
+CinemaShared
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaShared";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaShared.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaShared</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">uk.ac.man.bioinf.apps.xml.XMLBootModule</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">uk.ac.man.bioinf.apps.cinema.CinemaBoot</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaShared</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaShared</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A></DL>
+
+<P>
+CinemaShared.java
+
+
+ Created: Tue Sep 12 17:22:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaShared.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html#CinemaShared()">CinemaShared</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html#fetchMainBootName()">fetchMainBootName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaBoot"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#fetchModuleSystemIdentifier()">fetchModuleSystemIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#getXMLParserClass()">getXMLParserClass</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#load()">load</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#resolveXMLLoadName(java.lang.String)">resolveXMLLoadName</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#characters(java.lang.String)">characters</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#classEnd()">classEnd</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#configStart(org.xml.sax.Attributes)">configStart</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#enumerationEnd()">enumerationEnd</A>, <A HREF="../../../../../../uk/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#fi [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaShared()"><!-- --></A><H3>
+CinemaShared</H3>
+<PRE>
+public <B>CinemaShared</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="fetchMainBootName()"><!-- --></A><H3>
+fetchMainBootName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchMainBootName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html#fetchMainBootName()">fetchMainBootName</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaShared.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLBootModule">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html
new file mode 100644
index 0000000..efbbff7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html
@@ -0,0 +1,258 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:19 BST 2002 -->
+<TITLE>
+CinemaXMLParserFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaXMLParserFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaXMLParserFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema</FONT>
+<BR>
+Class CinemaXMLParserFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.CinemaXMLParserFactory</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaXMLParserFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A></DL>
+
+<P>
+CinemaXMLParserFactory.java
+
+
+ Created: Mon Sep 18 18:59:17 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaXMLParserFactory.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html#CinemaXMLParserFactory()">CinemaXMLParserFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> org.xml.sax.XMLReader</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html#getXMLParser()">getXMLParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaXMLParserFactory()"><!-- --></A><H3>
+CinemaXMLParserFactory</H3>
+<PRE>
+public <B>CinemaXMLParserFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getXMLParser()"><!-- --></A><H3>
+getXMLParser</H3>
+<PRE>
+public org.xml.sax.XMLReader <B>getXMLParser</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html#getXMLParser()">getXMLParser</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaXMLParserFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html
new file mode 100644
index 0000000..ede3f16
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html
@@ -0,0 +1,375 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:19 BST 2002 -->
+<TITLE>
+AminoAcidColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AminoAcidColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AminoAcidColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class AminoAcidColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AminoAcidColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+AminoAcidColorMapMetaData.java
+
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AminoAcidColorMapMetaData.java,v 1.4 2001/07/06 11:44:50 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#AminoAcidColorMapMetaData()">AminoAcidColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AminoAcidColorMapMetaData()"><!-- --></A><H3>
+AminoAcidColorMapMetaData</H3>
+<PRE>
+public <B>AminoAcidColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AminoAcidColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html
new file mode 100644
index 0000000..3fff57e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html
@@ -0,0 +1,466 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:19 BST 2002 -->
+<TITLE>
+CinemaColorFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaColorFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaColorFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class CinemaColorFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaColorFactory</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaColorFactory.java
+
+
+ Created: Fri Feb 9 11:49:21 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaColorFactory.java,v 1.5 2002/03/08 14:49:27 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#CinemaColorFactory()">CinemaColorFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#addMetaData(uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)">addMetaData</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A> colorMap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getColorMapIterator()">getColorMapIterator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getDefaultColorMapMetaData()">getDefaultColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getMetaData(uk.ac.man.bioinf.gui.color.ColorMap)">getMetaData</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> map)</CODE>
+
+<BR>
+ Returns a meta data object for the given ColorMap.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getMetaData(java.lang.String)">getMetaData</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getSize()">getSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaColorFactory()"><!-- --></A><H3>
+CinemaColorFactory</H3>
+<PRE>
+public <B>CinemaColorFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addMetaData(uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData)"><!-- --></A><H3>
+addMetaData</H3>
+<PRE>
+public void <B>addMetaData</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A> colorMap)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMetaData(uk.ac.man.bioinf.gui.color.ColorMap)"><!-- --></A><H3>
+getMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A> <B>getMetaData</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> map)</PRE>
+<DL>
+<DD>Returns a meta data object for the given ColorMap.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>map</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMetaData(java.lang.String)"><!-- --></A><H3>
+getMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A> <B>getMetaData</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapIterator()"><!-- --></A><H3>
+getColorMapIterator</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A> <B>getColorMapIterator</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSize()"><!-- --></A><H3>
+getSize</H3>
+<PRE>
+public int <B>getSize</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDefaultColorMapMetaData()"><!-- --></A><H3>
+getDefaultColorMapMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A> <B>getDefaultColorMapMetaData</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaColorFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html
new file mode 100644
index 0000000..abb936a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:19 BST 2002 -->
+<TITLE>
+CinemaColorIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaColorIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaColorIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class CinemaColorIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaColorIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaColorIdentifier.java
+
+
+ Created: Sun May 28 22:34:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaColorIdentifier.java,v 1.4 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html#CINEMA_COLOR_FACTORY">CINEMA_COLOR_FACTORY</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html#CINEMA_COLOR_SELECTOR">CINEMA_COLOR_SELECTOR</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_COLOR_FACTORY"><!-- --></A><H3>
+CINEMA_COLOR_FACTORY</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A> <B>CINEMA_COLOR_FACTORY</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_COLOR_SELECTOR"><!-- --></A><H3>
+CINEMA_COLOR_SELECTOR</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A> <B>CINEMA_COLOR_SELECTOR</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaColorIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html
new file mode 100644
index 0000000..c5ef349
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html
@@ -0,0 +1,403 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:19 BST 2002 -->
+<TITLE>
+CinemaColorSelector
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaColorSelector";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaColorSelector.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class CinemaColorSelector</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaColorSelector</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></DL>
+
+<P>
+CinemaColorSelector.java
+
+ Created: Sun May 28 22:14:13 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaColorSelector.java,v 1.8 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#CinemaColorSelector()">CinemaColorSelector</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getColorFactory()">getColorFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaColorSelector()"><!-- --></A><H3>
+CinemaColorSelector</H3>
+<PRE>
+public <B>CinemaColorSelector</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorFactory()"><!-- --></A><H3>
+getColorFactory</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html">CinemaColorFactory</A> <B>getColorFactory</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaColorSelector.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html
new file mode 100644
index 0000000..254518a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:19 BST 2002 -->
+<TITLE>
+ColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Interface ColorMapMetaData</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html">ColormapColorMapMetaData</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html">DefaultColorMapMetaData</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Gr [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ColorMapMetaData</B></DL>
+
+<P>
+ColorMapMetaData.java
+
+ Many of the colour maps available need to be treated in different
+ ways. So for instance some colour maps can use a single shared
+ instance, others needs a new one for each alignment. It does not
+ really make sense to try and encapsulate this sort of knowledge
+ within the ColorMap class, but it is needed within Cinema...
+
+ Created: Tue Jul 18 14:57:08 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorMapMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html
new file mode 100644
index 0000000..0d7fbf6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:20 BST 2002 -->
+<TITLE>
+ColormapColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColormapColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColormapColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class ColormapColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ColormapColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColormapColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#ColormapColorMapMetaData()">ColormapColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ColormapColorMapMetaData()"><!-- --></A><H3>
+ColormapColorMapMetaData</H3>
+<PRE>
+public <B>ColormapColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColormapColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html
new file mode 100644
index 0000000..aa52fe6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:20 BST 2002 -->
+<TITLE>
+DefaultColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class DefaultColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#DefaultColorMapMetaData()">DefaultColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultColorMapMetaData()"><!-- --></A><H3>
+DefaultColorMapMetaData</H3>
+<PRE>
+public <B>DefaultColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html
new file mode 100644
index 0000000..1cb5182
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:20 BST 2002 -->
+<TITLE>
+GrayScaleVariance
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GrayScaleVariance";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GrayScaleVariance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class GrayScaleVariance</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>GrayScaleVariance</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+GrayScaleVariance.java
+
+
+ Created: Fri Nov 30 13:58:29 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GrayScaleVariance.java,v 1.1 2002/03/08 14:49:40 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#GrayScaleVariance()">GrayScaleVariance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GrayScaleVariance()"><!-- --></A><H3>
+GrayScaleVariance</H3>
+<PRE>
+public <B>GrayScaleVariance</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GrayScaleVariance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html
new file mode 100644
index 0000000..d9bcac6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html
@@ -0,0 +1,311 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:20 BST 2002 -->
+<TITLE>
+InstancePerAlignmentColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InstancePerAlignmentColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InstancePerAlignmentColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class InstancePerAlignmentColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.InstancePerAlignmentColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>InstancePerAlignmentColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+InstancePerAlignmentColorMapMetaData.java
+
+
+ Created: Wed Jul 19 14:50:50 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InstancePerAlignmentColorMapMetaData.java,v 1.4 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#InstancePerAlignmentColorMapMetaData()">InstancePerAlignmentColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#createColorMapInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">createColorMapInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.seq [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InstancePerAlignmentColorMapMetaData()"><!-- --></A><H3>
+InstancePerAlignmentColorMapMetaData</H3>
+<PRE>
+public <B>InstancePerAlignmentColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="createColorMapInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+createColorMapInstance</H3>
+<PRE>
+protected abstract <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>createColorMapInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InstancePerAlignmentColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html
new file mode 100644
index 0000000..0a16e7f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:20 BST 2002 -->
+<TITLE>
+IntenseColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="IntenseColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntenseColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class IntenseColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>IntenseColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: IntenseColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#IntenseColorMapMetaData()">IntenseColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IntenseColorMapMetaData()"><!-- --></A><H3>
+IntenseColorMapMetaData</H3>
+<PRE>
+public <B>IntenseColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntenseColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html
new file mode 100644
index 0000000..8924b8e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+Js_TestColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Js_TestColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Js_TestColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class Js_TestColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>Js_TestColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Js_TestColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#Js_TestColorMapMetaData()">Js_TestColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.Js_TestColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Js_TestColorMapMetaData()"><!-- --></A><H3>
+Js_TestColorMapMetaData</H3>
+<PRE>
+public <B>Js_TestColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Js_TestColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html
new file mode 100644
index 0000000..ec0a2f0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+NullColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NullColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class NullColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.NullColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NullColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+NullColorMapMetaData.java
+
+
+ Created: Fri Jul 21 15:57:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NullColorMapMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#NullColorMapMetaData()">NullColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NullColorMapMetaData()"><!-- --></A><H3>
+NullColorMapMetaData</H3>
+<PRE>
+public <B>NullColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html
new file mode 100644
index 0000000..67e0943
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+PedanticColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PedanticColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PedanticColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class PedanticColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PedanticColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PedanticColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#PedanticColorMapMetaData()">PedanticColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PedanticColorMapMetaData()"><!-- --></A><H3>
+PedanticColorMapMetaData</H3>
+<PRE>
+public <B>PedanticColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PedanticColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html
new file mode 100644
index 0000000..9506b49
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+PercentageIDVarianceColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PercentageIDVarianceColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDVarianceColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class PercentageIDVarianceColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PercentageIDVarianceColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+PercentageIDVarianceColorMapMetaData.java
+
+
+ Created: Wed Jul 19 15:00:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PercentageIDVarianceColorMapMetaData.java,v 1.6 2001/05/08 17:37:52 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#PercentageIDVarianceColorMapMetaData()">PercentageIDVarianceColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PercentageIDVarianceColorMapMetaData()"><!-- --></A><H3>
+PercentageIDVarianceColorMapMetaData</H3>
+<PRE>
+public <B>PercentageIDVarianceColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDVarianceColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html
new file mode 100644
index 0000000..aa3e7fc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html
@@ -0,0 +1,396 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+TaylorColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="TaylorColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="TaylorColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class TaylorColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>TaylorColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: TaylorColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#TaylorColorMapMetaData()">TaylorColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="TaylorColorMapMetaData()"><!-- --></A><H3>
+TaylorColorMapMetaData</H3>
+<PRE>
+public <B>TaylorColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="TaylorColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html
new file mode 100644
index 0000000..a12a7ce
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+ThreadedPercentageIDVarianceColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ThreadedPercentageIDVarianceColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedPercentageIDVarianceColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class ThreadedPercentageIDVarianceColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ThreadedPercentageIDVarianceColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+ThreadedPercentageIDVarianceColorMapMetaData.java
+
+
+ Created: Fri Dec 1 16:54:24 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ThreadedPercentageIDVarianceColorMapMetaData.java,v 1.3 2001/05/08 17:37:59 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#ThreadedPercentageIDVarianceColorMapMetaData()">ThreadedPercentageIDVarianceColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ThreadedPercentageIDVarianceColorMapMetaData()"><!-- --></A><H3>
+ThreadedPercentageIDVarianceColorMapMetaData</H3>
+<PRE>
+public <B>ThreadedPercentageIDVarianceColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedPercentageIDVarianceColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html
new file mode 100644
index 0000000..98098d0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+VariableColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VariableColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VariableColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class VariableColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>VariableColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VariableColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#VariableColorMapMetaData()">VariableColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="VariableColorMapMetaData()"><!-- --></A><H3>
+VariableColorMapMetaData</H3>
+<PRE>
+public <B>VariableColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VariableColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html
new file mode 100644
index 0000000..235db78
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:21 BST 2002 -->
+<TITLE>
+VariationsColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VariationsColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VariationsColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class VariationsColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>VariationsColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VariationsColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#VariationsColorMapMetaData()">VariationsColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="VariationsColorMapMetaData()"><!-- --></A><H3>
+VariationsColorMapMetaData</H3>
+<PRE>
+public <B>VariationsColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VariationsColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html
new file mode 100644
index 0000000..ff6c21f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:22 BST 2002 -->
+<TITLE>
+WhiteColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="WhiteColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WhiteColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class WhiteColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.WhiteColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>WhiteColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+WhiteColorMapMetaData.java
+
+
+ Created: Fri Feb 9 13:12:26 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: WhiteColorMapMetaData.java,v 1.2 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#WhiteColorMapMetaData()">WhiteColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> cons,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="WhiteColorMapMetaData()"><!-- --></A><H3>
+WhiteColorMapMetaData</H3>
+<PRE>
+public <B>WhiteColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> cons,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>cons</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WhiteColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html
new file mode 100644
index 0000000..87b67bf
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:22 BST 2002 -->
+<TITLE>
+ZenecaColorMapMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ZenecaColorMapMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ZenecaColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.color</FONT>
+<BR>
+Class ZenecaColorMapMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ZenecaColorMapMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></DL>
+
+<P>
+THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ZenecaColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>color-convert.el</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#ZenecaColorMapMetaData()">ZenecaColorMapMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#getColorMapName()">getColorMapName</A></B>()</CODE>
+
+<BR>
+ This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns an instance of this type for this consensus sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ Returns a instance of this Color map for the given alignment
+ instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ZenecaColorMapMetaData()"><!-- --></A><H3>
+ZenecaColorMapMetaData</H3>
+<PRE>
+public <B>ZenecaColorMapMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMapName()"><!-- --></A><H3>
+getColorMapName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getColorMapName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>This should return the string that ColorMap instances created via
+ this class, return as their name, via the getName method
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getColorMapName()">getColorMapName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns a instance of this Color map for the given alignment
+ instance.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the ColorMap</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+getConsensusInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getConsensusInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></B></DD>
+<DD>Returns an instance of this type for this consensus sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html#getConsensusInstance(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">getConsensusInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the consensus sequence
+<DT><B>Returns:</B><DD>the ColorMap instance</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ZenecaColorMapMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-frame.html
new file mode 100644
index 0000000..5ec8274
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-frame.html
@@ -0,0 +1,79 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.color()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.color()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.color</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ColorMapMetaData.html" TARGET="classFrame"><I>ColorMapMetaData</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AminoAcidColorMapMetaData.html" TARGET="classFrame">AminoAcidColorMapMetaData</A>
+<BR>
+<A HREF="CinemaColorFactory.html" TARGET="classFrame">CinemaColorFactory</A>
+<BR>
+<A HREF="CinemaColorIdentifier.html" TARGET="classFrame">CinemaColorIdentifier</A>
+<BR>
+<A HREF="CinemaColorSelector.html" TARGET="classFrame">CinemaColorSelector</A>
+<BR>
+<A HREF="ColormapColorMapMetaData.html" TARGET="classFrame">ColormapColorMapMetaData</A>
+<BR>
+<A HREF="DefaultColorMapMetaData.html" TARGET="classFrame">DefaultColorMapMetaData</A>
+<BR>
+<A HREF="GrayScaleVariance.html" TARGET="classFrame">GrayScaleVariance</A>
+<BR>
+<A HREF="InstancePerAlignmentColorMapMetaData.html" TARGET="classFrame">InstancePerAlignmentColorMapMetaData</A>
+<BR>
+<A HREF="IntenseColorMapMetaData.html" TARGET="classFrame">IntenseColorMapMetaData</A>
+<BR>
+<A HREF="Js_TestColorMapMetaData.html" TARGET="classFrame">Js_TestColorMapMetaData</A>
+<BR>
+<A HREF="NullColorMapMetaData.html" TARGET="classFrame">NullColorMapMetaData</A>
+<BR>
+<A HREF="PedanticColorMapMetaData.html" TARGET="classFrame">PedanticColorMapMetaData</A>
+<BR>
+<A HREF="PercentageIDVarianceColorMapMetaData.html" TARGET="classFrame">PercentageIDVarianceColorMapMetaData</A>
+<BR>
+<A HREF="TaylorColorMapMetaData.html" TARGET="classFrame">TaylorColorMapMetaData</A>
+<BR>
+<A HREF="ThreadedPercentageIDVarianceColorMapMetaData.html" TARGET="classFrame">ThreadedPercentageIDVarianceColorMapMetaData</A>
+<BR>
+<A HREF="VariableColorMapMetaData.html" TARGET="classFrame">VariableColorMapMetaData</A>
+<BR>
+<A HREF="VariationsColorMapMetaData.html" TARGET="classFrame">VariationsColorMapMetaData</A>
+<BR>
+<A HREF="WhiteColorMapMetaData.html" TARGET="classFrame">WhiteColorMapMetaData</A>
+<BR>
+<A HREF="ZenecaColorMapMetaData.html" TARGET="classFrame">ZenecaColorMapMetaData</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-summary.html
new file mode 100644
index 0000000..419a44d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-summary.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.color()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.color()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.color
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorMapMetaData.html"><I>ColorMapMetaData</I></A></B></TD>
+<TD>ColorMapMetaData.java
+
+ Many of the colour maps available need to be treated in different
+ ways.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AminoAcidColorMapMetaData.html">AminoAcidColorMapMetaData</A></B></TD>
+<TD>AminoAcidColorMapMetaData.java
+
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaColorFactory.html">CinemaColorFactory</A></B></TD>
+<TD>CinemaColorFactory.java
+
+
+ Created: Fri Feb 9 11:49:21 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaColorIdentifier.html">CinemaColorIdentifier</A></B></TD>
+<TD>CinemaColorIdentifier.java
+
+
+ Created: Sun May 28 22:34:00 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaColorSelector.html">CinemaColorSelector</A></B></TD>
+<TD>CinemaColorSelector.java
+
+ Created: Sun May 28 22:14:13 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColormapColorMapMetaData.html">ColormapColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultColorMapMetaData.html">DefaultColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GrayScaleVariance.html">GrayScaleVariance</A></B></TD>
+<TD>GrayScaleVariance.java
+
+
+ Created: Fri Nov 30 13:58:29 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InstancePerAlignmentColorMapMetaData.html">InstancePerAlignmentColorMapMetaData</A></B></TD>
+<TD>InstancePerAlignmentColorMapMetaData.java
+
+
+ Created: Wed Jul 19 14:50:50 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="IntenseColorMapMetaData.html">IntenseColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Js_TestColorMapMetaData.html">Js_TestColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NullColorMapMetaData.html">NullColorMapMetaData</A></B></TD>
+<TD>NullColorMapMetaData.java
+
+
+ Created: Fri Jul 21 15:57:31 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PedanticColorMapMetaData.html">PedanticColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PercentageIDVarianceColorMapMetaData.html">PercentageIDVarianceColorMapMetaData</A></B></TD>
+<TD>PercentageIDVarianceColorMapMetaData.java
+
+
+ Created: Wed Jul 19 15:00:44 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="TaylorColorMapMetaData.html">TaylorColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ThreadedPercentageIDVarianceColorMapMetaData.html">ThreadedPercentageIDVarianceColorMapMetaData</A></B></TD>
+<TD>ThreadedPercentageIDVarianceColorMapMetaData.java
+
+
+ Created: Fri Dec 1 16:54:24 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VariableColorMapMetaData.html">VariableColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VariationsColorMapMetaData.html">VariationsColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="WhiteColorMapMetaData.html">WhiteColorMapMetaData</A></B></TD>
+<TD>WhiteColorMapMetaData.java
+
+
+ Created: Fri Feb 9 13:12:26 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ZenecaColorMapMetaData.html">ZenecaColorMapMetaData</A></B></TD>
+<TD>THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+
+ Created: Wed Jul 19 14:31:39 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-tree.html
new file mode 100644
index 0000000..1910afa
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/color/package-tree.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.color Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.color Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.color
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html"><B>CinemaColorIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.html"><B>AminoAcidColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.html"><B>ColormapColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.html"><B>DefaultColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.html"><B>GrayScaleVariance</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.html"><B>InstancePerAlignmentColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.html"><B>IntenseColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.html"><B>Js_TestColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.html"><B>CinemaColorFactory</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html"><B>CinemaColorSelector</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>)
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.html"><B>NullColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.html"><B>PedanticColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.html"><B>PercentageIDVarianceColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.html"><B>TaylorColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.html"><B>ThreadedPercentageIDVarianceColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.html"><B>VariableColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.html"><B>VariationsColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.html"><B>WhiteColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.html"><B>ZenecaColorMapMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html">ColorMapMetaData</A>)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.cinema.color.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.html"><B>ColorMapMetaData</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html
new file mode 100644
index 0000000..e549ebb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html
@@ -0,0 +1,431 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:22 BST 2002 -->
+<TITLE>
+CinemaConsensus
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaConsensus";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensus.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.consensus</FONT>
+<BR>
+Class CinemaConsensus</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaConsensus</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#CinemaConsensus()">CinemaConsensus</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Collection.html">Collection</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getAllMetaData()">getAllMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getDefaultMetaData()">getDefaultMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getMetaData(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)">getMetaData</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calc)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getMetaData(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)">getMetaData</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getMetaData(java.lang.String)">getMetaData</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaConsensus()"><!-- --></A><H3>
+CinemaConsensus</H3>
+<PRE>
+public <B>CinemaConsensus</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAllMetaData()"><!-- --></A><H3>
+getAllMetaData</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Collection.html">Collection</A> <B>getAllMetaData</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDefaultMetaData()"><!-- --></A><H3>
+getDefaultMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A> <B>getDefaultMetaData</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMetaData(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><!-- --></A><H3>
+getMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A> <B>getMetaData</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMetaData(uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator)"><!-- --></A><H3>
+getMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A> <B>getMetaData</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> calc)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMetaData(java.lang.String)"><!-- --></A><H3>
+getMetaData</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A> <B>getMetaData</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensus.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html
new file mode 100644
index 0000000..c81939b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:22 BST 2002 -->
+<TITLE>
+CinemaConsensusCalculatorMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaConsensusCalculatorMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensusCalculatorMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.consensus</FONT>
+<BR>
+Interface CinemaConsensusCalculatorMetaData</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>CinemaConsensusCalculatorMetaData</B></DL>
+
+<P>
+CinemaConsensusCalculatorMetaData.java
+
+
+ Created: Thu Jul 27 16:45:21 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaConsensusCalculatorMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getConsensusCalculatorName()">getConsensusCalculatorName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusCalculatorName()"><!-- --></A><H3>
+getConsensusCalculatorName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getConsensusCalculatorName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensusCalculatorMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html
new file mode 100644
index 0000000..93862c7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html
@@ -0,0 +1,453 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:22 BST 2002 -->
+<TITLE>
+CinemaConsensusDisplay
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaConsensusDisplay";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensusDisplay.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.consensus</FONT>
+<BR>
+Class CinemaConsensusDisplay</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">Prop [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaConsensusDisplay</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DL>
+
+<P>
+CinemaConsensusDisplay.java
+
+
+ Created: Thu Nov 9 15:06:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaConsensusDisplay.java,v 1.10 2001/05/22 15:50:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#CinemaConsensusDisplay()">CinemaConsensusDisplay</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getConsensusModule()">getConsensusModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaConsensusDisplay()"><!-- --></A><H3>
+CinemaConsensusDisplay</H3>
+<PRE>
+public <B>CinemaConsensusDisplay</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusModule()"><!-- --></A><H3>
+getConsensusModule</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html">CinemaConsensus</A> <B>getConsensusModule</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensusDisplay.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html
new file mode 100644
index 0000000..4b32897
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:23 BST 2002 -->
+<TITLE>
+CinemaConsensusIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaConsensusIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensusIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.consensus</FONT>
+<BR>
+Class CinemaConsensusIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaConsensusIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaConsensusIdentifier.java
+
+
+ Created: Mon Jul 24 18:55:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaConsensusIdentifier.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html#CINEMA_CONSENSUS">CINEMA_CONSENSUS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html#CINEMA_CONSENSUS_DISPLAY">CINEMA_CONSENSUS_DISPLAY</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_CONSENSUS"><!-- --></A><H3>
+CINEMA_CONSENSUS</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A> <B>CINEMA_CONSENSUS</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_CONSENSUS_DISPLAY"><!-- --></A><H3>
+CINEMA_CONSENSUS_DISPLAY</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A> <B>CINEMA_CONSENSUS_DISPLAY</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaConsensusIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html
new file mode 100644
index 0000000..8d06737
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html
@@ -0,0 +1,349 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:23 BST 2002 -->
+<TITLE>
+PercentageIDConsensusCalculatorMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PercentageIDConsensusCalculatorMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDConsensusCalculatorMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.consensus</FONT>
+<BR>
+Class PercentageIDConsensusCalculatorMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PercentageIDConsensusCalculatorMetaData</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></DL>
+
+<P>
+PercentageIDConsensusCalculatorMetaData.java
+
+
+ Created: Thu Jul 27 16:46:59 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PercentageIDConsensusCalculatorMetaData.java,v 1.6 2001/05/08 17:39:16 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#PercentageIDConsensusCalculatorMetaData()">PercentageIDConsensusCalculatorMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getCalculatorInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getCalculatorInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getConsensusCalculatorName()">getConsensusCalculatorName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getMetaDataInstance()">getMetaDataInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PercentageIDConsensusCalculatorMetaData()"><!-- --></A><H3>
+PercentageIDConsensusCalculatorMetaData</H3>
+<PRE>
+public <B>PercentageIDConsensusCalculatorMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getMetaDataInstance()"><!-- --></A><H3>
+getMetaDataInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A> <B>getMetaDataInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCalculatorInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+getCalculatorInstance</H3>
+<PRE>
+protected <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.html">ConsensusCalculator</A> <B>getCalculatorInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusCalculatorName()"><!-- --></A><H3>
+getConsensusCalculatorName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getConsensusCalculatorName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getConsensusCalculatorName()">getConsensusCalculatorName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentageIDConsensusCalculatorMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html
new file mode 100644
index 0000000..b3e8a45
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html
@@ -0,0 +1,313 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:23 BST 2002 -->
+<TITLE>
+ThreadedPercentageIDConsensusCalculatorMetaData
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ThreadedPercentageIDConsensusCalculatorMetaData";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedPercentageIDConsensusCalculatorMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.consensus</FONT>
+<BR>
+Class ThreadedPercentageIDConsensusCalculatorMetaData</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ThreadedPercentageIDConsensusCalculatorMetaData</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A></DL>
+
+<P>
+ThreadedPercentageIDConsensusCalculatorMetaData.java
+
+
+ Created: Wed Nov 8 15:01:52 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ThreadedPercentageIDConsensusCalculatorMetaData.java,v 1.6 2001/05/08 17:39:16 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#ThreadedPercentageIDConsensusCalculatorMetaData()">ThreadedPercentageIDConsensusCalculatorMetaData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#getConsensusCalculatorName()">getConsensusCalculatorName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getInstance</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getCalculatorInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getCalculatorInstance</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html#getMetaDataInstance()">getMetaDataInstance</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ThreadedPercentageIDConsensusCalculatorMetaData()"><!-- --></A><H3>
+ThreadedPercentageIDConsensusCalculatorMetaData</H3>
+<PRE>
+public <B>ThreadedPercentageIDConsensusCalculatorMetaData</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A> module)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#setModule(uk.ac.man.bioinf.apps.cinema.CinemaModule)">setModule</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/Per [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> <B>getInstance</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getInstance(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">getInstance</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cine [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConsensusCalculatorName()"><!-- --></A><H3>
+getConsensusCalculatorName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getConsensusCalculatorName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html#getConsensusCalculatorName()">getConsensusCalculatorName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/Percentage [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedPercentageIDConsensusCalculatorMetaData.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-frame.html
new file mode 100644
index 0000000..ff731e0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-frame.html
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.consensus()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.consensus()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.consensus</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaConsensusCalculatorMetaData.html" TARGET="classFrame"><I>CinemaConsensusCalculatorMetaData</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaConsensus.html" TARGET="classFrame">CinemaConsensus</A>
+<BR>
+<A HREF="CinemaConsensusDisplay.html" TARGET="classFrame">CinemaConsensusDisplay</A>
+<BR>
+<A HREF="CinemaConsensusIdentifier.html" TARGET="classFrame">CinemaConsensusIdentifier</A>
+<BR>
+<A HREF="PercentageIDConsensusCalculatorMetaData.html" TARGET="classFrame">PercentageIDConsensusCalculatorMetaData</A>
+<BR>
+<A HREF="ThreadedPercentageIDConsensusCalculatorMetaData.html" TARGET="classFrame">ThreadedPercentageIDConsensusCalculatorMetaData</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html
new file mode 100644
index 0000000..6a7d9f4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html
@@ -0,0 +1,179 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.consensus()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.consensus()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.consensus
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaConsensusCalculatorMetaData.html"><I>CinemaConsensusCalculatorMetaData</I></A></B></TD>
+<TD>CinemaConsensusCalculatorMetaData.java
+
+
+ Created: Thu Jul 27 16:45:21 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaConsensus.html">CinemaConsensus</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaConsensusDisplay.html">CinemaConsensusDisplay</A></B></TD>
+<TD>CinemaConsensusDisplay.java
+
+
+ Created: Thu Nov 9 15:06:00 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaConsensusIdentifier.html">CinemaConsensusIdentifier</A></B></TD>
+<TD>CinemaConsensusIdentifier.java
+
+
+ Created: Mon Jul 24 18:55:00 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PercentageIDConsensusCalculatorMetaData.html">PercentageIDConsensusCalculatorMetaData</A></B></TD>
+<TD>PercentageIDConsensusCalculatorMetaData.java
+
+
+ Created: Thu Jul 27 16:46:59 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ThreadedPercentageIDConsensusCalculatorMetaData.html">ThreadedPercentageIDConsensusCalculatorMetaData</A></B></TD>
+<TD>ThreadedPercentageIDConsensusCalculatorMetaData.java
+
+
+ Created: Wed Nov 8 15:01:52 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html
new file mode 100644
index 0000000..ebc2c5a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html
@@ -0,0 +1,155 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.consensus Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.consensus Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.consensus
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html"><B>CinemaConsensusIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.html"><B>CinemaConsensus</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html"><B>CinemaConsensusDisplay</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.html"><B>PercentageIDConsensusCalculatorMetaData</B></A> (implements uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html">CinemaConsensusCalculatorMetaData</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.html"><B>ThreadedPercentageIDConsensusCalculatorMetaData</B></A></UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.cinema.consensus.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.html"><B>CinemaConsensusCalculatorMetaData</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html
new file mode 100644
index 0000000..dc6633b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html
@@ -0,0 +1,434 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:25 BST 2002 -->
+<TITLE>
+AlignmentToListCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentToListCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentToListCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.DefaultListCellRenderer">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.DefaultListCellRenderer">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class AlignmentToListCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">javax.swing.JLabel</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html">javax.swing.DefaultListCellRenderer</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListCellRenderer.html">ListCellRenderer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://j [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignmentToListCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html">DefaultListCellRenderer</A></DL>
+
+<P>
+AlignmentToListCellRenderer.java
+
+
+ Created: Tue May 16 18:02:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentToListCellRenderer.java,v 1.3 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.cinema.core.AlignmentToListCellRenderer">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.DefaultListCellRenderer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html">DefaultListCellRenderer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.UIResource.html">DefaultListCellRenderer.UIResource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JLabel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.AccessibleJLabel.html">JLabel.AccessibleJLabel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.DefaultListCellRenderer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html">DefaultListCellRenderer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html#noFocusBorder">noFocusBorder</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JLabel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#labelFor">labelFor</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.SwingConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#CENTER">CENTER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#EAST">EAST</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#HORIZONTAL">HORIZONTAL</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html#AlignmentToListCellRenderer()">AlignmentToListCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html#getListCellRendererComponent(javax.swing.JList, java.lang.Object, int, boolean, boolean)">getListCellRendererComponent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A> list,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.DefaultListCellRenderer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html">DefaultListCellRenderer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html#firePropertyChange(java.lang.String, boolean, boolean)">firePropertyChange</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html#firePropertyChange(java.lang.String, byte, byte)">firePropertyChange</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html#firePropertyChange(java.lang.String, cha [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JLabel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#checkHorizontalKey(int, java.lang.String)">checkHorizontalKey</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#checkVerticalKey(int, java.lang.String)">checkVerticalKey</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swin [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentToListCellRenderer()"><!-- --></A><H3>
+AlignmentToListCellRenderer</H3>
+<PRE>
+public <B>AlignmentToListCellRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getListCellRendererComponent(javax.swing.JList, java.lang.Object, int, boolean, boolean)"><!-- --></A><H3>
+getListCellRendererComponent</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> <B>getListCellRendererComponent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A> list,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>getListCellRendererComponent</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListCellRenderer.html">ListCellRenderer</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html#getListCellRendererComponent(javax.swing.JList, java.lang.Object, int, boolean, boolean)">getListCellRendererComponent</A></CODE> in class <CODE><A HREF="http: [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentToListCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.DefaultListCellRenderer">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.DefaultListCellRenderer">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html
new file mode 100644
index 0000000..41b9aa9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html
@@ -0,0 +1,345 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:26 BST 2002 -->
+<TITLE>
+AlignmentToListModel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentToListModel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentToListModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_javax.swing.AbstractListModel">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class AlignmentToListModel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">javax.swing.AbstractListModel</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignmentToListModel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">AbstractListModel</A></DL>
+
+<P>
+AlignmentToListModel.java
+
+
+ Created: Tue May 16 17:55:45 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentToListModel.java,v 1.2 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.cinema.core.AlignmentToListModel">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.AbstractListModel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">AbstractListModel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#listenerList">listenerList</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#AlignmentToListModel(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">AlignmentToListModel</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#addListDataListener(javax.swing.event.ListDataListener)">addListDataListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListDataListener.html">ListDataListener</A> l)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#getSize()">getSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html#removeListDataListener(javax.swing.event.ListDataListener)">removeListDataListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListDataListener.html">ListDataListener</A> l)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.AbstractListModel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">AbstractListModel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#fireContentsChanged(java.lang.Object, int, int)">fireContentsChanged</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#fireIntervalAdded(java.lang.Object, int, int)">fireIntervalAdded</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#fireIntervalRemoved(java.lang.Object, int, int)">fireIntervalRemoved [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentToListModel(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+AlignmentToListModel</H3>
+<PRE>
+public <B>AlignmentToListModel</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSize()"><!-- --></A><H3>
+getSize</H3>
+<PRE>
+public int <B>getSize</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addListDataListener(javax.swing.event.ListDataListener)"><!-- --></A><H3>
+addListDataListener</H3>
+<PRE>
+public void <B>addListDataListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListDataListener.html">ListDataListener</A> l)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>addListDataListener</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#addListDataListener(javax.swing.event.ListDataListener)">addListDataListener</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel. [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeListDataListener(javax.swing.event.ListDataListener)"><!-- --></A><H3>
+removeListDataListener</H3>
+<PRE>
+public void <B>removeListDataListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListDataListener.html">ListDataListener</A> l)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>removeListDataListener</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#removeListDataListener(javax.swing.event.ListDataListener)">removeListDataListener</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractL [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentToListModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_javax.swing.AbstractListModel">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html
new file mode 100644
index 0000000..9dc8e3f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html
@@ -0,0 +1,214 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:25 BST 2002 -->
+<TITLE>
+CinemaActionProvider
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaActionProvider";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaActionProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Interface CinemaActionProvider</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.html">CinemaConsensusDisplay</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html" [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>CinemaActionProvider</B></DL>
+
+<P>
+CinemaActionProvider.java
+
+
+ Created: Tue May 16 16:32:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaActionProvider.java,v 1.2 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaActionProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html
new file mode 100644
index 0000000..079db8e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html
@@ -0,0 +1,714 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:26 BST 2002 -->
+<TITLE>
+CinemaCoreGui
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaCoreGui";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCoreGui.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaCoreGui</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaCoreGui</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DL>
+
+<P>
+CinemaCoreGui.java
+
+ This module defines the core Gui for cinema. It gives access to all
+ of the main components that it defines, and get/set methods for
+ these. This is meant to be a pretty low level module. Generally
+ other modules should not use this unless absolutely
+ necessary. Rather the CinemaCoreView module should be used instead.
+
+ At the moment set access has not been provided to any of the
+ components. I may change this if is needed.
+
+ Created: Wed Apr 19 16:58:08 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaCoreGui.java,v 1.17 2001/05/08 17:39:31 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.apps.systemevents.SystemListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#NO_VETO">NO_VETO</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_ERROR">VETO_DUE_TO_ERROR</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_USER_REQUEST">VETO_DUE_TO_USER_REQUEST</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#CinemaCoreGui()">CinemaCoreGui</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#attemptSystemExit()">attemptSystemExit</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ The method called, from an external source, to remove this module
+ and prepare it for garbage collection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getAlignmentFrame()">getAlignmentFrame</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getFrame()">getFrame</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getJMenuBar()">getJMenuBar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRowHeaders()">getRowHeaders</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRuler()">getRuler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getRulerPanel()">getRulerPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getScrollPane()">getScrollPane</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getStatusBar()">getStatusBar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#getViewer()">getViewer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> event)</CODE>
+
+<BR>
+ This is an event listener for system events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html#systemListenerPriority()">systemListenerPriority</A></B>()</CODE>
+
+<BR>
+ Some events (particularly shut downs) have to happen in a
+ very specific order.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaCoreGui()"><!-- --></A><H3>
+CinemaCoreGui</H3>
+<PRE>
+public <B>CinemaCoreGui</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><!-- --></A><H3>
+systemEventOccured</H3>
+<PRE>
+public void <B>systemEventOccured</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> event)
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></B></DD>
+<DD>This is an event listener for system events. All listeners
+ should be signalled before the SystemEvent occurs. They should
+ not return from this method until they are ready for that event
+ to occur. An exception is thrown if the listener wishes to
+ veto this system event. g
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the system event occuring
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></CODE> - if the listener does not want the event to happen</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemListenerPriority()"><!-- --></A><H3>
+systemListenerPriority</H3>
+<PRE>
+public int <B>systemListenerPriority</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></B></DD>
+<DD>Some events (particularly shut downs) have to happen in a
+ very specific order. This method provides a priority to
+ allow this to happen. Those with the lowest priority are
+ informed first. Any valid int value is acceptable.
+ This interface does not provide the ability to set different priorities
+ for different events. The same effect can be achieved by delegating the
+ to a small class. This way a single object can register more than one
+ listener object, and thus have different priorities for different events
+ A listener should not change its priority. There is not guarentee when
+ this value will be used.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemListenerPriority()">systemListenerPriority</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFrame()"><!-- --></A><H3>
+getFrame</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> <B>getFrame</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRowHeaders()"><!-- --></A><H3>
+getRowHeaders</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A> <B>getRowHeaders</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getJMenuBar()"><!-- --></A><H3>
+getJMenuBar</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A> <B>getJMenuBar</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollPane()"><!-- --></A><H3>
+getScrollPane</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>getScrollPane</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRulerPanel()"><!-- --></A><H3>
+getRulerPanel</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>getRulerPanel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getViewer()"><!-- --></A><H3>
+getViewer</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>getViewer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRuler()"><!-- --></A><H3>
+getRuler</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A> <B>getRuler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getStatusBar()"><!-- --></A><H3>
+getStatusBar</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A> <B>getStatusBar</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignmentFrame()"><!-- --></A><H3>
+getAlignmentFrame</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> <B>getAlignmentFrame</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="attemptSystemExit()"><!-- --></A><H3>
+attemptSystemExit</H3>
+<PRE>
+public void <B>attemptSystemExit</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCoreGui.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html
new file mode 100644
index 0000000..516575c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html
@@ -0,0 +1,328 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:27 BST 2002 -->
+<TITLE>
+CinemaCoreIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaCoreIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCoreIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaCoreIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaCoreIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaCoreIdentifier.java
+
+
+ Created: Sun May 7 18:16:43 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaCoreIdentifier.java,v 1.6 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_GO">CINEMA_GO</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_MENU_SYSTEM">CINEMA_MENU_SYSTEM</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_SEQUENCE_MENU">CINEMA_SEQUENCE_MENU</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html#CINEMA_SYSTEM_EVENTS">CINEMA_SYSTEM_EVENTS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_GO"><!-- --></A><H3>
+CINEMA_GO</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A> <B>CINEMA_GO</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_SYSTEM_EVENTS"><!-- --></A><H3>
+CINEMA_SYSTEM_EVENTS</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A> <B>CINEMA_SYSTEM_EVENTS</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_MENU_SYSTEM"><!-- --></A><H3>
+CINEMA_MENU_SYSTEM</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A> <B>CINEMA_MENU_SYSTEM</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_SEQUENCE_MENU"><!-- --></A><H3>
+CINEMA_SEQUENCE_MENU</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html">CinemaCoreIdentifier</A> <B>CINEMA_SEQUENCE_MENU</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCoreIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html
new file mode 100644
index 0000000..bcdfc1c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html
@@ -0,0 +1,733 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:27 BST 2002 -->
+<TITLE>
+CinemaCoreView
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaCoreView";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCoreView.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaCoreView</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaCoreView</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></DL>
+
+<P>
+CinemaCoreView.java
+
+ This class provides an easy interface to many of the display
+ functions of Cinema. (PENDING:- PL) In time this should actually be
+ turned into an interface. The idea is that all modules should use
+ this class rather than the CinemaCoreGui class, because there is
+ nothing here which refers to swing which means that we could
+ replace the gui implementation with an entirely different gui, and
+ still reuse many of the modules.
+
+ Created: Wed Apr 19 22:00:36 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaCoreView.java,v 1.13 2001/04/11 17:04:41 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#CinemaCoreView()">CinemaCoreView</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Add a listener specifically interested in events connected with the MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a listener interested in vetoing multiple sequence alignment
+ specific events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">clearSequenceTitleColor</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ The method called, from an external source, to remove this module
+ and prepare it for garbage collection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getAlignmentSelectionModel()">getAlignmentSelectionModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getColorMap()">getColorMap</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getSequenceAlignment()">getSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#sendStatusMessage(java.lang.String)">sendStatusMessage</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ Send a message to the status bar.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)">setAlignmentSelectionModel</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> model)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)">setColorMap</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> map)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ Set the Sequence Alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)">setSequenceTitleColor</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> colour)</CODE>
+
+<BR>
+ This sets the colour that is used to display the sequence
+ title.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRowHeaders()">getRowHeaders</A>, <A HREF="../../../../../ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#fireCinemaPropertyChang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaCoreView()"><!-- --></A><H3>
+CinemaCoreView</H3>
+<PRE>
+public <B>CinemaCoreView</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setSequenceAlignment</H3>
+<PRE>
+public void <B>setSequenceAlignment</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></B></DD>
+<DD>Set the Sequence Alignment. Signals a property change event.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAlignment()"><!-- --></A><H3>
+getSequenceAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSequenceAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getSequenceAlignment()">getSequenceAlignment</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)"><!-- --></A><H3>
+setAlignmentSelectionModel</H3>
+<PRE>
+public void <B>setAlignmentSelectionModel</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> model)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setAlignmentSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)">setAlignmentSelectionModel</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignmentSelectionModel()"><!-- --></A><H3>
+getAlignmentSelectionModel</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> <B>getAlignmentSelectionModel</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getAlignmentSelectionModel()">getAlignmentSelectionModel</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)"><!-- --></A><H3>
+setColorMap</H3>
+<PRE>
+public void <B>setColorMap</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> map)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)">setColorMap</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMap()"><!-- --></A><H3>
+getColorMap</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getColorMap</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getColorMap()">getColorMap</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)"><!-- --></A><H3>
+setSequenceTitleColor</H3>
+<PRE>
+public void <B>setSequenceTitleColor</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> colour)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></B></DD>
+<DD>This sets the colour that is used to display the sequence
+ title. NOT the colour of the elements! This is usually done to
+ display some linkage between sequences of the same colour.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#setSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)">setSequenceTitleColor</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - <DD><CODE>colour</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+clearSequenceTitleColor</H3>
+<PRE>
+public void <B>clearSequenceTitleColor</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#clearSequenceTitleColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">clearSequenceTitleColor</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="sendStatusMessage(java.lang.String)"><!-- --></A><H3>
+sendStatusMessage</H3>
+<PRE>
+public void <B>sendStatusMessage</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD>Send a message to the status bar. This message should be for
+ minor information only as it can get overrun at any stage.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#sendStatusMessage(java.lang.String)">sendStatusMessage</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>message</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Add a listener specifically interested in events connected with the MSA.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/ [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/c [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Adds a listener interested in vetoing multiple sequence alignment
+ specific events.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a vetoable multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a vetoable multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../.. [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCoreView.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html
new file mode 100644
index 0000000..53b2148
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html
@@ -0,0 +1,214 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:25 BST 2002 -->
+<TITLE>
+CinemaFramedActionProvider
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaFramedActionProvider";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaFramedActionProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Interface CinemaFramedActionProvider</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.html">CinemaColorSelector</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html">CinemaRegexp</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html">CinemaResizeElements</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>CinemaFramedActionProvider</B></DL>
+
+<P>
+CinemaFramedActionProvider.java
+
+
+ Created: Fri Oct 13 17:04:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaFramedActionProvider.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaFramedActionProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html
new file mode 100644
index 0000000..0e155a3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html
@@ -0,0 +1,338 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:27 BST 2002 -->
+<TITLE>
+CinemaGo
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGo";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGo.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaGo</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaGo</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaGo</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></DL>
+
+<P>
+CinemaGo.java
+
+ This class actually makes the Cinema gui visible. Effectively its a
+ dummy module, which I wrote so that I make the gui pop up when it
+ is fully formed rather than building it whilst its on
+ screen. Eventually I would like it to do some more things,
+ particularly provide a progress bar (although I do not know how I
+ am going to find out what is going on. An event scheme for the
+ ModuleFactory? How will I know how many modules are going to be loaded?)
+
+ Created: Sat May 27 00:37:17 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGo.java,v 1.7 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html#CinemaGo()">CinemaGo</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaGo()"><!-- --></A><H3>
+CinemaGo</H3>
+<PRE>
+public <B>CinemaGo</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGo.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html
new file mode 100644
index 0000000..50dc84b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html
@@ -0,0 +1,360 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaMenuSystem
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaMenuSystem";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMenuSystem.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaMenuSystem</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaMenuSystem</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></DL>
+
+<P>
+CinemaMenuSystem.java
+
+
+ Created: Tue May 16 14:24:27 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaMenuSystem.java,v 1.7 2001/05/08 17:39:44 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#CinemaMenuSystem()">CinemaMenuSystem</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaMenuSystem()"><!-- --></A><H3>
+CinemaMenuSystem</H3>
+<PRE>
+public <B>CinemaMenuSystem</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMenuSystem.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html
new file mode 100644
index 0000000..bf20ed6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaModuleCoreIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaModuleCoreIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaModuleCoreIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaModuleCoreIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaModuleCoreIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaModuleCoreIdentifer.java
+
+
+ Created: Fri May 26 21:39:17 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaModuleCoreIdentifier.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html#CINEMA_CORE_GUI">CINEMA_CORE_GUI</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html#CINEMA_CORE_VIEW">CINEMA_CORE_VIEW</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_CORE_GUI"><!-- --></A><H3>
+CINEMA_CORE_GUI</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A> <B>CINEMA_CORE_GUI</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_CORE_VIEW"><!-- --></A><H3>
+CINEMA_CORE_VIEW</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A> <B>CINEMA_CORE_VIEW</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaModuleCoreIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html
new file mode 100644
index 0000000..9e99266
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html
@@ -0,0 +1,388 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaSequenceMenu
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaSequenceMenu";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSequenceMenu.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaSequenceMenu</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaSequenceMenu</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></DL>
+
+<P>
+CinemaSequenceMenu.java
+
+
+ Created: Mon May 22 14:04:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaSequenceMenu.java,v 1.8 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#CinemaSequenceMenu()">CinemaSequenceMenu</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#add(javax.swing.JMenuItem)">add</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> menu)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#getLastSequence()">getLastSequence</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html">JPopupMenu</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#getPopupMenu()">getPopupMenu</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaSequenceMenu()"><!-- --></A><H3>
+CinemaSequenceMenu</H3>
+<PRE>
+public <B>CinemaSequenceMenu</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPopupMenu()"><!-- --></A><H3>
+getPopupMenu</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html">JPopupMenu</A> <B>getPopupMenu</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="add(javax.swing.JMenuItem)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public void <B>add</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> menu)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLastSequence()"><!-- --></A><H3>
+getLastSequence</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getLastSequence</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSequenceMenu.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html
new file mode 100644
index 0000000..c18db5d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html
@@ -0,0 +1,413 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaSystemEvents
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaSystemEvents";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSystemEvents.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class CinemaSystemEvents</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaSystemEvents</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></DL>
+
+<P>
+CinemaSystemEvents.java
+
+
+ Created: Thu Apr 20 18:26:56 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaSystemEvents.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#CinemaSystemEvents()">CinemaSystemEvents</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">addSystemEventListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#fireSystemEvent(uk.ac.man.bioinf.apps.systemevents.SystemEventOption)">fireSystemEvent</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> option)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#fireSystemExit(int)">fireSystemExit</A></B>(int i)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">removeSystemEventListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Mo [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaSystemEvents()"><!-- --></A><H3>
+CinemaSystemEvents</H3>
+<PRE>
+public <B>CinemaSystemEvents</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><!-- --></A><H3>
+addSystemEventListener</H3>
+<PRE>
+public void <B>addSystemEventListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">addSystemEventListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><!-- --></A><H3>
+removeSystemEventListener</H3>
+<PRE>
+public void <B>removeSystemEventListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">removeSystemEventListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireSystemEvent(uk.ac.man.bioinf.apps.systemevents.SystemEventOption)"><!-- --></A><H3>
+fireSystemEvent</H3>
+<PRE>
+public void <B>fireSystemEvent</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> option)
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireSystemExit(int)"><!-- --></A><H3>
+fireSystemExit</H3>
+<PRE>
+public void <B>fireSystemExit</B>(int i)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSystemEvents.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html
new file mode 100644
index 0000000..dd53d90
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html
@@ -0,0 +1,348 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+VersionInformation
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VersionInformation";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VersionInformation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core</FONT>
+<BR>
+Class VersionInformation</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.VersionInformation</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>VersionInformation</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+VersionInformation.java
+
+ This provides standard information about this version of Cinema.
+
+ Created: Wed Apr 19 17:03:28 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VersionInformation.java,v 1.21 2002/04/20 15:03:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#VersionInformation()">VersionInformation</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getAboutText()">getAboutText</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getAuthorString()">getAuthorString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getAuthorURLs()">getAuthorURLs</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getMaintainerURL()">getMaintainerURL</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getProjectURL()">getProjectURL</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html#getVersionNumber()">getVersionNumber</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="VersionInformation()"><!-- --></A><H3>
+VersionInformation</H3>
+<PRE>
+public <B>VersionInformation</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getVersionNumber()"><!-- --></A><H3>
+getVersionNumber</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersionNumber</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getProjectURL()"><!-- --></A><H3>
+getProjectURL</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getProjectURL</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAboutText()"><!-- --></A><H3>
+getAboutText</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getAboutText</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAuthorURLs()"><!-- --></A><H3>
+getAuthorURLs</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A>[] <B>getAuthorURLs</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAuthorString()"><!-- --></A><H3>
+getAuthorString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getAuthorString</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMaintainerURL()"><!-- --></A><H3>
+getMaintainerURL</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getMaintainerURL</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VersionInformation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-frame.html
new file mode 100644
index 0000000..e1c490b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-frame.html
@@ -0,0 +1,65 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.core()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.core()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.core</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaActionProvider.html" TARGET="classFrame"><I>CinemaActionProvider</I></A>
+<BR>
+<A HREF="CinemaFramedActionProvider.html" TARGET="classFrame"><I>CinemaFramedActionProvider</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentToListCellRenderer.html" TARGET="classFrame">AlignmentToListCellRenderer</A>
+<BR>
+<A HREF="AlignmentToListModel.html" TARGET="classFrame">AlignmentToListModel</A>
+<BR>
+<A HREF="CinemaCoreGui.html" TARGET="classFrame">CinemaCoreGui</A>
+<BR>
+<A HREF="CinemaCoreIdentifier.html" TARGET="classFrame">CinemaCoreIdentifier</A>
+<BR>
+<A HREF="CinemaCoreView.html" TARGET="classFrame">CinemaCoreView</A>
+<BR>
+<A HREF="CinemaGo.html" TARGET="classFrame">CinemaGo</A>
+<BR>
+<A HREF="CinemaMenuSystem.html" TARGET="classFrame">CinemaMenuSystem</A>
+<BR>
+<A HREF="CinemaModuleCoreIdentifier.html" TARGET="classFrame">CinemaModuleCoreIdentifier</A>
+<BR>
+<A HREF="CinemaSequenceMenu.html" TARGET="classFrame">CinemaSequenceMenu</A>
+<BR>
+<A HREF="CinemaSystemEvents.html" TARGET="classFrame">CinemaSystemEvents</A>
+<BR>
+<A HREF="VersionInformation.html" TARGET="classFrame">VersionInformation</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-summary.html
new file mode 100644
index 0000000..dcffdc3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-summary.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.core()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.core()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.core
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaActionProvider.html"><I>CinemaActionProvider</I></A></B></TD>
+<TD>CinemaActionProvider.java
+
+
+ Created: Tue May 16 16:32:25 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaFramedActionProvider.html"><I>CinemaFramedActionProvider</I></A></B></TD>
+<TD>CinemaFramedActionProvider.java
+
+
+ Created: Fri Oct 13 17:04:25 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentToListCellRenderer.html">AlignmentToListCellRenderer</A></B></TD>
+<TD>AlignmentToListCellRenderer.java
+
+
+ Created: Tue May 16 18:02:22 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentToListModel.html">AlignmentToListModel</A></B></TD>
+<TD>AlignmentToListModel.java
+
+
+ Created: Tue May 16 17:55:45 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaCoreGui.html">CinemaCoreGui</A></B></TD>
+<TD>CinemaCoreGui.java
+
+ This module defines the core Gui for cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaCoreIdentifier.html">CinemaCoreIdentifier</A></B></TD>
+<TD>CinemaCoreIdentifier.java
+
+
+ Created: Sun May 7 18:16:43 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaCoreView.html">CinemaCoreView</A></B></TD>
+<TD>CinemaCoreView.java
+
+ This class provides an easy interface to many of the display
+ functions of Cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGo.html">CinemaGo</A></B></TD>
+<TD>CinemaGo.java
+
+ This class actually makes the Cinema gui visible.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaMenuSystem.html">CinemaMenuSystem</A></B></TD>
+<TD>CinemaMenuSystem.java
+
+
+ Created: Tue May 16 14:24:27 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaModuleCoreIdentifier.html">CinemaModuleCoreIdentifier</A></B></TD>
+<TD>CinemaModuleCoreIdentifer.java
+
+
+ Created: Fri May 26 21:39:17 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaSequenceMenu.html">CinemaSequenceMenu</A></B></TD>
+<TD>CinemaSequenceMenu.java
+
+
+ Created: Mon May 22 14:04:57 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaSystemEvents.html">CinemaSystemEvents</A></B></TD>
+<TD>CinemaSystemEvents.java
+
+
+ Created: Thu Apr 20 18:26:56 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VersionInformation.html">VersionInformation</A></B></TD>
+<TD>VersionInformation.java
+
+ This provides standard information about this version of Cinema.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-tree.html
new file mode 100644
index 0000000..d07ab3c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/package-tree.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.core Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.core Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.core
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.html"><B>CinemaCoreIdentifier</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.html"><B>CinemaModuleCoreIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html"><B>AbstractListModel</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.html"><B>AlignmentToListModel</B></A></UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html"><B>JLabel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/DefaultListCellRenderer.html"><B>DefaultListCellRenderer</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListCellRenderer.html">ListCellRenderer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.html"><B>AlignmentToListCellRenderer</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html"><B>CinemaCoreGui</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html"><B>CinemaSystemEvents</B></A> (implements uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html"><B>CinemaCoreView</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">Al [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaGo.html"><B>CinemaGo</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.html"><B>CinemaMenuSystem</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html"><B>CinemaSequence [...]
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/VersionInformation.html"><B>VersionInformation</B></A></UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html"><B>CinemaActionProvider</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html"><B>CinemaFramedActionProvider</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/consensus/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html
new file mode 100644
index 0000000..a2fbe35
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html
@@ -0,0 +1,294 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaTestLaunch
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaTestLaunch";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaTestLaunch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core.test</FONT>
+<BR>
+Class CinemaTestLaunch</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaTestLaunch</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CinemaTestLaunch.java
+
+
+ Created: Wed Apr 19 18:29:17 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaTestLaunch.java,v 1.11 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#CinemaTestLaunch()">CinemaTestLaunch</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#generateColorMap()">generateColorMap</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#generateMsa()">generateMsa</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaTestLaunch()"><!-- --></A><H3>
+CinemaTestLaunch</H3>
+<PRE>
+public <B>CinemaTestLaunch</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="generateMsa()"><!-- --></A><H3>
+generateMsa</H3>
+<PRE>
+public static <A HREF="../../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>generateMsa</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="generateColorMap()"><!-- --></A><H3>
+generateColorMap</H3>
+<PRE>
+public static <A HREF="../../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>generateColorMap</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaTestLaunch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html
new file mode 100644
index 0000000..89be71f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html
@@ -0,0 +1,254 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaTestModuleLaunch
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaTestModuleLaunch";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaTestModuleLaunch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.core.test</FONT>
+<BR>
+Class CinemaTestModuleLaunch</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestModuleLaunch</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaTestModuleLaunch</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CinemaTestModuleLaunch.java
+
+
+ Created: Wed May 24 18:37:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaTestModuleLaunch.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html#CinemaTestModuleLaunch()">CinemaTestModuleLaunch</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaTestModuleLaunch()"><!-- --></A><H3>
+CinemaTestModuleLaunch</H3>
+<PRE>
+public <B>CinemaTestModuleLaunch</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaTestModuleLaunch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-frame.html
new file mode 100644
index 0000000..6374467
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.core.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.core.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.core.test</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaTestLaunch.html" TARGET="classFrame">CinemaTestLaunch</A>
+<BR>
+<A HREF="CinemaTestModuleLaunch.html" TARGET="classFrame">CinemaTestModuleLaunch</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html
new file mode 100644
index 0000000..b860c54
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.core.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.core.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.core.test
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaTestLaunch.html">CinemaTestLaunch</A></B></TD>
+<TD>CinemaTestLaunch.java
+
+
+ Created: Wed Apr 19 18:29:17 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaTestModuleLaunch.html">CinemaTestModuleLaunch</A></B></TD>
+<TD>CinemaTestModuleLaunch.java
+
+
+ Created: Wed May 24 18:37:22 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html
new file mode 100644
index 0000000..b684eb4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.core.test Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.core.test Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.core.test
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.html"><B>CinemaTestLaunch</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.core.test.<A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.html"><B>CinemaTestModuleLaunch</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/core/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html
new file mode 100644
index 0000000..aec2db1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html
@@ -0,0 +1,372 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:23 BST 2002 -->
+<TITLE>
+CinemaAnchorManager
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaAnchorManager";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaAnchorManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.group</FONT>
+<BR>
+Class CinemaAnchorManager</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.group.CinemaAnchorManager</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaAnchorManager</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DL>
+
+<P>
+CinemaAnchorManager.java
+
+ This group takes care of the anchoring groups, and adding and
+ removing appropriate listeners to the main alignment viewer, and
+ then adding and removing gaps.
+
+
+ Created: Wed Feb 21 18:36:38 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaAnchorManager.java,v 1.3 2001/07/06 11:45:51 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#CinemaAnchorManager(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)">CinemaAnchorManager</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#anchorAll()">anchorAll</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#anchorGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)">anchorGroup</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#isAnchored(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)">isAnchored</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#unanchorAll()">unanchorAll</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html#unanchorGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)">unanchorGroup</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaAnchorManager(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)"><!-- --></A><H3>
+CinemaAnchorManager</H3>
+<PRE>
+public <B>CinemaAnchorManager</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> module)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="anchorGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><!-- --></A><H3>
+anchorGroup</H3>
+<PRE>
+public void <B>anchorGroup</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="anchorAll()"><!-- --></A><H3>
+anchorAll</H3>
+<PRE>
+public void <B>anchorAll</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="unanchorGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><!-- --></A><H3>
+unanchorGroup</H3>
+<PRE>
+public void <B>unanchorGroup</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="unanchorAll()"><!-- --></A><H3>
+unanchorAll</H3>
+<PRE>
+public void <B>unanchorAll</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isAnchored(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><!-- --></A><H3>
+isAnchored</H3>
+<PRE>
+public boolean <B>isAnchored</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaAnchorManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html
new file mode 100644
index 0000000..ea91b4e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html
@@ -0,0 +1,362 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:23 BST 2002 -->
+<TITLE>
+CinemaGroup
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGroup";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.group</FONT>
+<BR>
+Class CinemaGroup</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.group.CinemaGroup</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSeq [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaGroup</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A></DL>
+
+<P>
+CinemaGroup.java
+
+ This class is more or less entirely a wrapper around the
+ HashMap, and just switches all of the return types back to
+ something sane.
+ Created: Mon May 22 17:42:36 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGroup.java,v 1.7 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#CinemaGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.lang.String)">CinemaGroup</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A> manager,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#getColor()">getColor</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#setColor(java.awt.Color)">setColor</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> groupColor)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html#setTitle(java.lang.String)">setTitle</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequenceListe [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#getGappedSequences()">getGappedSequences</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.lang.String)"><!-- --></A><H3>
+CinemaGroup</H3>
+<PRE>
+public <B>CinemaGroup</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A> manager,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setTitle(java.lang.String)"><!-- --></A><H3>
+setTitle</H3>
+<PRE>
+public void <B>setTitle</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColor()"><!-- --></A><H3>
+getColor</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColor</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setColor(java.awt.Color)"><!-- --></A><H3>
+setColor</H3>
+<PRE>
+public void <B>setColor</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> groupColor)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getIdentifier()">getIdentifier</A></CODE> in class <CODE><A HREF="../../../../../. [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html
new file mode 100644
index 0000000..1f1d5c0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html
@@ -0,0 +1,528 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:24 BST 2002 -->
+<TITLE>
+CinemaGroupFrame
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGroupFrame";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.group</FONT>
+<BR>
+Class CinemaGroupFrame</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">java.awt.Window</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">java.awt.Frame</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">javax.swing.JFrame</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">uk.ac.man.bioinf.gui.optionable.OptionableJFrame</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaGroupFrame</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionListener.html">ListSelectionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event [...]
+
+<P>
+CinemaGroupFrame.java
+
+
+ Created: Fri Jun 2 19:19:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGroupFrame.java,v 1.17 2001/07/10 13:40:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.AccessibleJFrame.html">JFrame.AccessibleJFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.AccessibleAWTFrame.html">Frame.AccessibleAWTFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.AccessibleAWTWindow.html">Window.AccessibleAWTWindow</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#EXIT_ON_CLOSE">EXIT_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPane">rootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPaneCheckingEnabled">rootPaneCheckingEnabled</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#CROSSHAIR_CURSOR">CROSSHAIR_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#DEFAULT_CURSOR">DEFAULT_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#E_RESIZE_CURSOR">E_RESIZE_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#HAND_CURSOR">HAND_CURSOR</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html">WindowConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DISPOSE_ON_CLOSE">DISPOSE_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DO_NOTHING_ON_CLOSE">DO_NOTHING_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#HIDE_ON_CLOSE">HIDE_ON_CLOSE</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#CinemaGroupFrame(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)">CinemaGroupFrame</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html#valueChanged(javax.swing.event.ListSelectionEvent)">valueChanged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionEvent.html">ListSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.optionable.OptionableJFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#defaultPack()">defaultPack</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#forceOptionable()">forceOptionable</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getDefaultOptionHandler()">getDefaultOptionHandler</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptionGroupName [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#createRootPane()">createRootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#frameInit()">frameInit</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#getAccessibleContext()">getAccessib [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getCursorType()">getCursorType</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getExtendedState()">getExtendedState</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addWindowFocusListener(java.awt.event.WindowFocusL [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#getFont()">getFont</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#postEvent(java.awt.Event)">postEvent</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaGroupFrame(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)"><!-- --></A><H3>
+CinemaGroupFrame</H3>
+<PRE>
+public <B>CinemaGroupFrame</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> module)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="valueChanged(javax.swing.event.ListSelectionEvent)"><!-- --></A><H3>
+valueChanged</H3>
+<PRE>
+public void <B>valueChanged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionEvent.html">ListSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>valueChanged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionListener.html">ListSelectionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html
new file mode 100644
index 0000000..a25f47f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:24 BST 2002 -->
+<TITLE>
+CinemaGroupIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGroupIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.group</FONT>
+<BR>
+Class CinemaGroupIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.group.CinemaGroupIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaGroupIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaGroupIdentifier.java
+
+
+ Created: Thu May 25 18:53:58 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGroupIdentifier.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html">CinemaGroupIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html#CINEMA_GROUPS">CINEMA_GROUPS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_GROUPS"><!-- --></A><H3>
+CINEMA_GROUPS</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html">CinemaGroupIdentifier</A> <B>CINEMA_GROUPS</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html
new file mode 100644
index 0000000..aa8a51c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html
@@ -0,0 +1,642 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:24 BST 2002 -->
+<TITLE>
+CinemaGroupManager
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGroupManager";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.group</FONT>
+<BR>
+Class CinemaGroupManager</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaGroupManager</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CinemaGroupManager.java
+
+
+ Created: Mon May 22 17:36:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGroupManager.java,v 1.9 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#groupsName">groupsName</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#groupsOrder">groupsOrder</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#CinemaGroupManager(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)">CinemaGroupManager</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#clearGroups()">clearGroups</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#createNewGroup()">createNewGroup</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#createNewGroup(java.lang.String)">createNewGroup</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#createNewGroup(java.lang.String, java.awt.Color)">createNewGroup</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> colour)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#firePropertyChange(java.beans.PropertyChangeEvent)">firePropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#firePropertyChange(java.lang.String, int, int)">firePropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ int oldValue,
+ int newValue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)">firePropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> oldValue,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> newValue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getAllGroups()">getAllGroups</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getGroupByName(java.lang.String)">getGroupByName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ Returns group with name or null</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getGroupContaining(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getGroupContaining</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#hasListeners(java.lang.String)">hasListeners</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#removeGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)">removeGroup</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#removePropertyChangeListener(java.beans.PropertyChangeListener)">removePropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">removePropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html#swapGroupOrder(int, int)">swapGroupOrder</A></B>(int a,
+ int b)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="groupsName"><!-- --></A><H3>
+groupsName</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>groupsName</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager.groupsName">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="groupsOrder"><!-- --></A><H3>
+groupsOrder</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>groupsOrder</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager.groupsOrder">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaGroupManager(uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule)"><!-- --></A><H3>
+CinemaGroupManager</H3>
+<PRE>
+public <B>CinemaGroupManager</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A> module)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAllGroups()"><!-- --></A><H3>
+getAllGroups</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A>[] <B>getAllGroups</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGroupByName(java.lang.String)"><!-- --></A><H3>
+getGroupByName</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> <B>getGroupByName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD>Returns group with name or null
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createNewGroup(java.lang.String, java.awt.Color)"><!-- --></A><H3>
+createNewGroup</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> <B>createNewGroup</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> colour)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createNewGroup(java.lang.String)"><!-- --></A><H3>
+createNewGroup</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> <B>createNewGroup</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createNewGroup()"><!-- --></A><H3>
+createNewGroup</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> <B>createNewGroup</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGroupContaining(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getGroupContaining</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> <B>getGroupContaining</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeGroup(uk.ac.man.bioinf.apps.cinema.group.CinemaGroup)"><!-- --></A><H3>
+removeGroup</H3>
+<PRE>
+public void <B>removeGroup</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A> group)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="swapGroupOrder(int, int)"><!-- --></A><H3>
+swapGroupOrder</H3>
+<PRE>
+public void <B>swapGroupOrder</B>(int a,
+ int b)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearGroups()"><!-- --></A><H3>
+clearGroups</H3>
+<PRE>
+public void <B>clearGroups</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addPropertyChangeListener(java.beans.PropertyChangeListener)"><!-- --></A><H3>
+addPropertyChangeListener</H3>
+<PRE>
+public void <B>addPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removePropertyChangeListener(java.beans.PropertyChangeListener)"><!-- --></A><H3>
+removePropertyChangeListener</H3>
+<PRE>
+public void <B>removePropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><!-- --></A><H3>
+addPropertyChangeListener</H3>
+<PRE>
+public void <B>addPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><!-- --></A><H3>
+removePropertyChangeListener</H3>
+<PRE>
+public void <B>removePropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+firePropertyChange</H3>
+<PRE>
+protected void <B>firePropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> oldValue,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> newValue)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firePropertyChange(java.lang.String, int, int)"><!-- --></A><H3>
+firePropertyChange</H3>
+<PRE>
+protected void <B>firePropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ int oldValue,
+ int newValue)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firePropertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+firePropertyChange</H3>
+<PRE>
+protected void <B>firePropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="hasListeners(java.lang.String)"><!-- --></A><H3>
+hasListeners</H3>
+<PRE>
+public boolean <B>hasListeners</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html
new file mode 100644
index 0000000..f0a8e06
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html
@@ -0,0 +1,553 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:25 BST 2002 -->
+<TITLE>
+CinemaGroupModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaGroupModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.group</FONT>
+<BR>
+Class CinemaGroupModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html" [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaGroupModule</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">Propert [...]
+
+<P>
+CinemaGroupModule.java
+
+
+ Created: Tue May 23 15:42:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaGroupModule.java,v 1.15 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#CinemaGroupModule()">CinemaGroupModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getAnchorManager()">getAnchorManager</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getGroupManager()">getGroupManager</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getLastSequence()">getLastSequence</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getMenuSystem()">getMenuSystem</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaGroupModule()"><!-- --></A><H3>
+CinemaGroupModule</H3>
+<PRE>
+public <B>CinemaGroupModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLastSequence()"><!-- --></A><H3>
+getLastSequence</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getLastSequence</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAnchorManager()"><!-- --></A><H3>
+getAnchorManager</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html">CinemaAnchorManager</A> <B>getAnchorManager</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGroupManager()"><!-- --></A><H3>
+getGroupManager</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html">CinemaGroupManager</A> <B>getGroupManager</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMenuSystem()"><!-- --></A><H3>
+getMenuSystem</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.html">CinemaSequenceMenu</A> <B>getMenuSystem</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaGroupModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-frame.html
new file mode 100644
index 0000000..a0b3387
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-frame.html
@@ -0,0 +1,42 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.group()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.group()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.group</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaAnchorManager.html" TARGET="classFrame">CinemaAnchorManager</A>
+<BR>
+<A HREF="CinemaGroup.html" TARGET="classFrame">CinemaGroup</A>
+<BR>
+<A HREF="CinemaGroupFrame.html" TARGET="classFrame">CinemaGroupFrame</A>
+<BR>
+<A HREF="CinemaGroupIdentifier.html" TARGET="classFrame">CinemaGroupIdentifier</A>
+<BR>
+<A HREF="CinemaGroupManager.html" TARGET="classFrame">CinemaGroupManager</A>
+<BR>
+<A HREF="CinemaGroupModule.html" TARGET="classFrame">CinemaGroupModule</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-summary.html
new file mode 100644
index 0000000..c3fadfb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-summary.html
@@ -0,0 +1,174 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.group()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.group()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.group
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaAnchorManager.html">CinemaAnchorManager</A></B></TD>
+<TD>CinemaAnchorManager.java
+
+ This group takes care of the anchoring groups, and adding and
+ removing appropriate listeners to the main alignment viewer, and
+ then adding and removing gaps.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGroup.html">CinemaGroup</A></B></TD>
+<TD>CinemaGroup.java
+
+ This class is more or less entirely a wrapper around the
+ HashMap, and just switches all of the return types back to
+ something sane.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGroupFrame.html">CinemaGroupFrame</A></B></TD>
+<TD>CinemaGroupFrame.java
+
+
+ Created: Fri Jun 2 19:19:00 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGroupIdentifier.html">CinemaGroupIdentifier</A></B></TD>
+<TD>CinemaGroupIdentifier.java
+
+
+ Created: Thu May 25 18:53:58 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGroupManager.html">CinemaGroupManager</A></B></TD>
+<TD>CinemaGroupManager.java
+
+
+ Created: Mon May 22 17:36:04 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGroupModule.html">CinemaGroupModule</A></B></TD>
+<TD>CinemaGroupModule.java
+
+
+ Created: Tue May 23 15:42:48 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-tree.html
new file mode 100644
index 0000000..373ea5f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/group/package-tree.html
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.group Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.group Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.group
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.html"><B>CinemaGroupIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html"><B>AbstractGappedSequenceGroup</B></A> (implements uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html"><B>GroupSequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlig [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html"><B>CinemaGroup</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.html"><B>CinemaAnchorManager</B></A> (implements java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.html"><B>CinemaGroupManager</B></A><LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/produc [...]
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>OptionableJFrame</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html"><B>CinemaGroupFrame</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, javax.swing.event. [...]
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.group.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html"><B>CinemaGroupModule</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf [...]
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html
new file mode 100644
index 0000000..b0b53e5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html
@@ -0,0 +1,540 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:35 BST 2002 -->
+<TITLE>
+AbstractSequenceInput
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequenceInput";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceInput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class AbstractSequenceInput</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html">FileSequenceInput</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequenceInput</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DL>
+
+<P>
+This class is abstract and will be extended by any sequence input
+ modules. It merely provides the action stuff for the menu system,
+ and describes an abstract method run by the actionPerformed(...)
+ and implemented by the children of this class.
+
+
+ Created: Wed Jun 14 15:26:56 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequenceInput.java,v 1.13 2002/04/20 14:59:05 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#eh">eh</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#AbstractSequenceInput()">AbstractSequenceInput</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ Supplies the action for the menu system/whatever else wishes to
+ invoke this modules action.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getAvailableParsers()">getAvailableParsers</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getExceptionHandler()">getExceptionHandler</A></B>()</CODE>
+
+<BR>
+ Returns the parser exception handler.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getParser(java.lang.String)">getParser</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getParserDescription(java.lang.String)">getParserDescription</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#openAlignment()">openAlignment</A></B>()</CODE>
+
+<BR>
+ Obtains the sequence alignment by the relevent method.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#setExceptionHandler(uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler)">setExceptionHandler</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A> exceptionHandler)</CODE>
+
+<BR>
+ Sets the parser exception handler.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="eh"><!-- --></A><H3>
+eh</H3>
+<PRE>
+protected <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A> <B>eh</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequenceInput()"><!-- --></A><H3>
+AbstractSequenceInput</H3>
+<PRE>
+public <B>AbstractSequenceInput</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAvailableParsers()"><!-- --></A><H3>
+getAvailableParsers</H3>
+<PRE>
+public final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] <B>getAvailableParsers</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParser(java.lang.String)"><!-- --></A><H3>
+getParser</H3>
+<PRE>
+public final <A HREF="../../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A> <B>getParser</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParserDescription(java.lang.String)"><!-- --></A><H3>
+getParserDescription</H3>
+<PRE>
+public final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getParserDescription</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD>Supplies the action for the menu system/whatever else wishes to
+ invoke this modules action.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the possible actions</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="openAlignment()"><!-- --></A><H3>
+openAlignment</H3>
+<PRE>
+public abstract <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>openAlignment</B>()</PRE>
+<DL>
+<DD>Obtains the sequence alignment by the relevent method.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setExceptionHandler(uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler)"><!-- --></A><H3>
+setExceptionHandler</H3>
+<PRE>
+public void <B>setExceptionHandler</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A> exceptionHandler)</PRE>
+<DL>
+<DD>Sets the parser exception handler.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getExceptionHandler()"><!-- --></A><H3>
+getExceptionHandler</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> <B>getExceptionHandler</B>()</PRE>
+<DL>
+<DD>Returns the parser exception handler.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the exception handler</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceInput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html
new file mode 100644
index 0000000..a2712eb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:35 BST 2002 -->
+<TITLE>
+AbstractSequenceInputParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequenceInputParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceInputParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class AbstractSequenceInputParserExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html">FileSequenceInputParserExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequenceInputParserExceptionHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DL>
+
+<P>
+AbstractSequenceInputParserExceptionHandler provides methods so
+ that the exceptions can be stored and at a later date shown all
+ together. This is the intended methodology to be used for Cinema.
+
+
+ Created: Fri Jun 16 14:06:51 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequenceInputParserExceptionHandler.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#AbstractSequenceInputParserExceptionHandler()">AbstractSequenceInputParserExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#clearExceptions()">clearExceptions</A></B>()</CODE>
+
+<BR>
+ Clears all exceptions that have been stored.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#getParserExceptions()">getParserExceptions</A></B>()</CODE>
+
+<BR>
+ Return the stored exceptions, so that they can be displayed all
+ together.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#storeException(uk.ac.man.bioinf.io.ParserException)">storeException</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</CODE>
+
+<BR>
+ Stores the exception, so that later a call can be made to
+ getParserExceptions() in order to display all the exceptions
+ together.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.ParserExceptionHandler"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.io.<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequenceInputParserExceptionHandler()"><!-- --></A><H3>
+AbstractSequenceInputParserExceptionHandler</H3>
+<PRE>
+public <B>AbstractSequenceInputParserExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="storeException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+storeException</H3>
+<PRE>
+public void <B>storeException</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</PRE>
+<DL>
+<DD>Stores the exception, so that later a call can be made to
+ getParserExceptions() in order to display all the exceptions
+ together. The normal exception handler will just store the
+ exception and allow a gap to be inserted in the sequence.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the parser exception</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParserExceptions()"><!-- --></A><H3>
+getParserExceptions</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A>[] <B>getParserExceptions</B>()</PRE>
+<DL>
+<DD>Return the stored exceptions, so that they can be displayed all
+ together.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the exceptions</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearExceptions()"><!-- --></A><H3>
+clearExceptions</H3>
+<PRE>
+public void <B>clearExceptions</B>()</PRE>
+<DL>
+<DD>Clears all exceptions that have been stored.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceInputParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html
new file mode 100644
index 0000000..afe828f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html
@@ -0,0 +1,549 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:35 BST 2002 -->
+<TITLE>
+AbstractSequenceOutput
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequenceOutput";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceOutput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class AbstractSequenceOutput</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html">FileSequenceOutput</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequenceOutput</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DL>
+
+<P>
+This class is abstract and will be extended by any sequence output
+ modules. It merely provides the action stuff for the menu system,
+ and describes an abstract method run by the actionPerformed(...)
+ and implemented by the children of this class.
+
+
+ Created: Mon Jul 31 22:22:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequenceOutput.java,v 1.5 2001/07/06 11:48:08 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#eh">eh</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#AbstractSequenceOutput()">AbstractSequenceOutput</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getAvailableParsers()">getAvailableParsers</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getExceptionHandler()">getExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getParser(java.lang.String)">getParser</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getParserDescription(java.lang.String)">getParserDescription</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">saveAlignment</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">saveAlignmentAs</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#setExceptionHandler(uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler)">setExceptionHandler</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A> exceptionHandler)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="eh"><!-- --></A><H3>
+eh</H3>
+<PRE>
+protected <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A> <B>eh</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequenceOutput()"><!-- --></A><H3>
+AbstractSequenceOutput</H3>
+<PRE>
+public <B>AbstractSequenceOutput</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAvailableParsers()"><!-- --></A><H3>
+getAvailableParsers</H3>
+<PRE>
+public final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] <B>getAvailableParsers</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParser(java.lang.String)"><!-- --></A><H3>
+getParser</H3>
+<PRE>
+public final <A HREF="../../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A> <B>getParser</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParserDescription(java.lang.String)"><!-- --></A><H3>
+getParserDescription</H3>
+<PRE>
+public final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getParserDescription</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyOfParser)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+saveAlignment</H3>
+<PRE>
+public abstract void <B>saveAlignment</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+saveAlignmentAs</H3>
+<PRE>
+public abstract void <B>saveAlignmentAs</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setExceptionHandler(uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler)"><!-- --></A><H3>
+setExceptionHandler</H3>
+<PRE>
+public void <B>setExceptionHandler</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A> exceptionHandler)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getExceptionHandler()"><!-- --></A><H3>
+getExceptionHandler</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> <B>getExceptionHandler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceOutput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html
new file mode 100644
index 0000000..80b4222
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:36 BST 2002 -->
+<TITLE>
+AbstractSequenceParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequenceParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class AbstractSequenceParserExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html">FileSequenceParserExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequenceParserExceptionHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DL>
+
+<P>
+AbstractSequenceInputParserExceptionHandler provides methods so
+ that the exceptions can be stored and at a later date shown all
+ together. This is the intended methodology to be used for Cinema.
+
+
+ Created: Fri Jun 16 14:06:51 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequenceParserExceptionHandler.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#AbstractSequenceParserExceptionHandler()">AbstractSequenceParserExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#clearExceptions()">clearExceptions</A></B>()</CODE>
+
+<BR>
+ Clears all exceptions that have been stored.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#getParserExceptions()">getParserExceptions</A></B>()</CODE>
+
+<BR>
+ Return the stored exceptions, so that they can be displayed all
+ together.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#storeException(uk.ac.man.bioinf.io.ParserException)">storeException</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</CODE>
+
+<BR>
+ Stores the exception, so that later a call can be made to
+ getParserExceptions() in order to display all the exceptions
+ together.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.ParserExceptionHandler"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.io.<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequenceParserExceptionHandler()"><!-- --></A><H3>
+AbstractSequenceParserExceptionHandler</H3>
+<PRE>
+public <B>AbstractSequenceParserExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="storeException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+storeException</H3>
+<PRE>
+public void <B>storeException</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</PRE>
+<DL>
+<DD>Stores the exception, so that later a call can be made to
+ getParserExceptions() in order to display all the exceptions
+ together. The normal exception handler will just store the
+ exception and allow a gap to be inserted in the sequence.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the parser exception</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParserExceptions()"><!-- --></A><H3>
+getParserExceptions</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A>[] <B>getParserExceptions</B>()</PRE>
+<DL>
+<DD>Return the stored exceptions, so that they can be displayed all
+ together.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the exceptions</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearExceptions()"><!-- --></A><H3>
+clearExceptions</H3>
+<PRE>
+public void <B>clearExceptions</B>()</PRE>
+<DL>
+<DD>Clears all exceptions that have been stored.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html
new file mode 100644
index 0000000..c4c279e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html
@@ -0,0 +1,377 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:36 BST 2002 -->
+<TITLE>
+CinemaCommandLineParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaCommandLineParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCommandLineParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class CinemaCommandLineParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaCommandLineParser</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaCommandLineParser.java
+
+ This module is responsible for parsing the command line to Cinema
+ and invoking what ever actions are necessary.
+ <p>
+ <b>(PENDING: JNS)</b> 28-11-00 currently this is all hard coded and will
+ need to be altered and recompiled each time the command line
+ options are changed.
+ <p>
+
+ Created: Mon Nov 27 17:36:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaCommandLineParser.java,v 1.7 2001/05/24 15:39:13 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#CinemaCommandLineParser()">CinemaCommandLineParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#openFile(java.lang.String, java.lang.String)">openFile</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> filename,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> parser)</CODE>
+
+<BR>
+ Opens a declared file in Cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaCommandLineParser()"><!-- --></A><H3>
+CinemaCommandLineParser</H3>
+<PRE>
+public <B>CinemaCommandLineParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="openFile(java.lang.String, java.lang.String)"><!-- --></A><H3>
+openFile</H3>
+<PRE>
+public void <B>openFile</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> filename,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> parser)</PRE>
+<DL>
+<DD>Opens a declared file in Cinema.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>filename</CODE> - the filename<DD><CODE>parser</CODE> - the parser to use</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCommandLineParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html
new file mode 100644
index 0000000..334f9fc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:36 BST 2002 -->
+<TITLE>
+CinemaCommandLineParserIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaCommandLineParserIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCommandLineParserIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class CinemaCommandLineParserIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParserIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaCommandLineParserIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+The identifier for the CinemaCommandLineParser module.
+
+
+ Created: Thu Dec 21 12:34:24 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaCommandLineParserIdentifier.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html">CinemaCommandLineParserIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html#COMMAND_LINE_PARSER">COMMAND_LINE_PARSER</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="COMMAND_LINE_PARSER"><!-- --></A><H3>
+COMMAND_LINE_PARSER</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html">CinemaCommandLineParserIdentifier</A> <B>COMMAND_LINE_PARSER</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaCommandLineParserIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html
new file mode 100644
index 0000000..aeb8914
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html
@@ -0,0 +1,419 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:36 BST 2002 -->
+<TITLE>
+FileSequenceInput
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FileSequenceInput";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceInput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class FileSequenceInput</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileSequenceInput</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A></DL>
+
+<P>
+FileSequenceInput is a that module covers sequence input into
+ Cinema via files. It extends the abstract sequence input module
+ which provides the basics of any sequence input method into
+ Cinema. It is currently Cinema only the abstract sequence input
+ module extends the Cinema GUI module.
+
+
+ Created: Thu Jun 15 15:07:12 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FileSequenceInput.java,v 1.15 2002/04/20 14:58:56 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#eh">eh</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#FileSequenceInput()">FileSequenceInput</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#openAlignment()">openAlignment</A></B>()</CODE>
+
+<BR>
+ Obtains the sequence alignment by the relevent method.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#openFile(java.io.File, uk.ac.man.bioinf.io.AlignmentInputParser, uk.ac.man.bioinf.sequence.identifier.Identifier)">openFile</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A> parser,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ Opens a file using a parser.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getActions()">getActions</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getAvailableParsers()">getAvailableParsers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#getExceptionHandler()">getExceptionHandler</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html# [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileSequenceInput()"><!-- --></A><H3>
+FileSequenceInput</H3>
+<PRE>
+public <B>FileSequenceInput</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="openFile(java.io.File, uk.ac.man.bioinf.io.AlignmentInputParser, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+openFile</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>openFile</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A> parser,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD>Opens a file using a parser. This method was generated to allow
+ file parsing without the need for the open dialog - i.e., it will
+ make the passing of arguments to Cinema of the file name a lot
+ easier, or even possible.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>file</CODE> - the file<DD><CODE>parser</CODE> - the input parser<DD><CODE>ident</CODE> - the identifier for the alignment
+<DT><B>Returns:</B><DD>the sequence alignment
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="openAlignment()"><!-- --></A><H3>
+openAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>openAlignment</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A></CODE></B></DD>
+<DD>Obtains the sequence alignment by the relevent method.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html#openAlignment()">openAlignment</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html">AbstractSequenceInput</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceInput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html
new file mode 100644
index 0000000..4b4ff88
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:36 BST 2002 -->
+<TITLE>
+FileSequenceInputParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FileSequenceInputParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceInputParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class FileSequenceInputParserExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.FileSequenceInputParserExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileSequenceInputParserExceptionHandler</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A></DL>
+
+<P>
+FileSequenceInputParserExceptionHandler handles parser exceptions
+ to do with parsing files, and will display a dialog box.
+
+
+ Created: Thu Jun 15 23:39:37 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FileSequenceInputParserExceptionHandler.java,v 1.5 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html#FileSequenceInputParserExceptionHandler()">FileSequenceInputParserExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</CODE>
+
+<BR>
+ Handles exceptions thrown by a sequence parser.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInputParserExceptionHandler"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#clearExceptions()">clearExceptions</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#getParserExceptions()">getParserExceptions</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html#storeException(uk.ac.man.bioinf.io.ParserException)">storeExc [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileSequenceInputParserExceptionHandler()"><!-- --></A><H3>
+FileSequenceInputParserExceptionHandler</H3>
+<PRE>
+public <B>FileSequenceInputParserExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+handleException</H3>
+<PRE>
+public void <B>handleException</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></B></DD>
+<DD>Handles exceptions thrown by a sequence parser.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the exception</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceInputParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html
new file mode 100644
index 0000000..cba7bec
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html
@@ -0,0 +1,379 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:36 BST 2002 -->
+<TITLE>
+FileSequenceOutput
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FileSequenceOutput";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceOutput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class FileSequenceOutput</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileSequenceOutput</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A></DL>
+
+<P>
+FileSequenceOutput is a module that covers sequence output to a
+ file from Cinema. It extends the abstract sequence output module
+ that provides the basics of any sequence output from Cinema.
+
+
+ Created: Mon Jul 31 22:18:18 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FileSequenceOutput.java,v 1.7 2001/05/29 13:01:31 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#eh">eh</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#FileSequenceOutput()">FileSequenceOutput</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">saveAlignment</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html#saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">saveAlignmentAs</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getActions()">getActions</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getAvailableParsers()">getAvailableParsers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#getExceptionHandler()">getExceptionHandler</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileSequenceOutput()"><!-- --></A><H3>
+FileSequenceOutput</H3>
+<PRE>
+public <B>FileSequenceOutput</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+saveAlignment</H3>
+<PRE>
+public void <B>saveAlignment</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#saveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">saveAlignment</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+saveAlignmentAs</H3>
+<PRE>
+public void <B>saveAlignmentAs</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html#saveAlignmentAs(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">saveAlignmentAs</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html">AbstractSequenceOutput</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceOutput.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html
new file mode 100644
index 0000000..9ba8e62
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+FileSequenceParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FileSequenceParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class FileSequenceParserExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.FileSequenceParserExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileSequenceParserExceptionHandler</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A></DL>
+
+<P>
+FileSequenceParserExceptionHandler handles parser exceptions
+ to do with parsing files, and will display a dialog box.
+
+
+ Created: Thu Jun 15 23:39:37 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FileSequenceParserExceptionHandler.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html#FileSequenceParserExceptionHandler()">FileSequenceParserExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</CODE>
+
+<BR>
+ Handles exceptions thrown by a sequence parser.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceParserExceptionHandler"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#clearExceptions()">clearExceptions</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#getParserExceptions()">getParserExceptions</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html#storeException(uk.ac.man.bioinf.io.ParserException)">storeException</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileSequenceParserExceptionHandler()"><!-- --></A><H3>
+FileSequenceParserExceptionHandler</H3>
+<PRE>
+public <B>FileSequenceParserExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+handleException</H3>
+<PRE>
+public void <B>handleException</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></B></DD>
+<DD>Handles exceptions thrown by a sequence parser.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the exception</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSequenceParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html
new file mode 100644
index 0000000..299d28d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html
@@ -0,0 +1,294 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+SequenceInputModuleIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceInputModuleIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceInputModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class SequenceInputModuleIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceInputModuleIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+A module interface identifier for sequence input. It will deligate
+ to the different protocols available (e.g: file input, http
+ input).
+
+
+ Created: Tue Jun 13 12:43:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceInputModuleIdentifier.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html#FILE_INPUT">FILE_INPUT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html#SEQ_INPUT">SEQ_INPUT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SEQ_INPUT"><!-- --></A><H3>
+SEQ_INPUT</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A> <B>SEQ_INPUT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="FILE_INPUT"><!-- --></A><H3>
+FILE_INPUT</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A> <B>FILE_INPUT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceInputModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html
new file mode 100644
index 0000000..735afc5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+SequenceOutputModuleIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceOutputModuleIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceOutputModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.io</FONT>
+<BR>
+Class SequenceOutputModuleIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceOutputModuleIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+SequenceOutputModuleIdentifier.java
+
+
+ Created: Fri Aug 11 15:06:07 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceOutputModuleIdentifier.java,v 1.3 2001/05/29 13:01:31 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html#FILE_OUTPUT">FILE_OUTPUT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html#SEQ_OUTPUT">SEQ_OUTPUT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SEQ_OUTPUT"><!-- --></A><H3>
+SEQ_OUTPUT</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A> <B>SEQ_OUTPUT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="FILE_OUTPUT"><!-- --></A><H3>
+FILE_OUTPUT</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A> <B>FILE_OUTPUT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceOutputModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-frame.html
new file mode 100644
index 0000000..fca31aa
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-frame.html
@@ -0,0 +1,54 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.io()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.io()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.io</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractSequenceInput.html" TARGET="classFrame">AbstractSequenceInput</A>
+<BR>
+<A HREF="AbstractSequenceInputParserExceptionHandler.html" TARGET="classFrame">AbstractSequenceInputParserExceptionHandler</A>
+<BR>
+<A HREF="AbstractSequenceOutput.html" TARGET="classFrame">AbstractSequenceOutput</A>
+<BR>
+<A HREF="AbstractSequenceParserExceptionHandler.html" TARGET="classFrame">AbstractSequenceParserExceptionHandler</A>
+<BR>
+<A HREF="CinemaCommandLineParser.html" TARGET="classFrame">CinemaCommandLineParser</A>
+<BR>
+<A HREF="CinemaCommandLineParserIdentifier.html" TARGET="classFrame">CinemaCommandLineParserIdentifier</A>
+<BR>
+<A HREF="FileSequenceInput.html" TARGET="classFrame">FileSequenceInput</A>
+<BR>
+<A HREF="FileSequenceInputParserExceptionHandler.html" TARGET="classFrame">FileSequenceInputParserExceptionHandler</A>
+<BR>
+<A HREF="FileSequenceOutput.html" TARGET="classFrame">FileSequenceOutput</A>
+<BR>
+<A HREF="FileSequenceParserExceptionHandler.html" TARGET="classFrame">FileSequenceParserExceptionHandler</A>
+<BR>
+<A HREF="SequenceInputModuleIdentifier.html" TARGET="classFrame">SequenceInputModuleIdentifier</A>
+<BR>
+<A HREF="SequenceOutputModuleIdentifier.html" TARGET="classFrame">SequenceOutputModuleIdentifier</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-summary.html
new file mode 100644
index 0000000..593c1fd
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-summary.html
@@ -0,0 +1,194 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.io()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.io()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.io
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequenceInput.html">AbstractSequenceInput</A></B></TD>
+<TD>This class is abstract and will be extended by any sequence input
+ modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A></B></TD>
+<TD>AbstractSequenceInputParserExceptionHandler provides methods so
+ that the exceptions can be stored and at a later date shown all
+ together.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequenceOutput.html">AbstractSequenceOutput</A></B></TD>
+<TD>This class is abstract and will be extended by any sequence output
+ modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A></B></TD>
+<TD>AbstractSequenceInputParserExceptionHandler provides methods so
+ that the exceptions can be stored and at a later date shown all
+ together.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaCommandLineParser.html">CinemaCommandLineParser</A></B></TD>
+<TD>CinemaCommandLineParser.java
+
+ This module is responsible for parsing the command line to Cinema
+ and invoking what ever actions are necessary.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaCommandLineParserIdentifier.html">CinemaCommandLineParserIdentifier</A></B></TD>
+<TD>The identifier for the CinemaCommandLineParser module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FileSequenceInput.html">FileSequenceInput</A></B></TD>
+<TD>FileSequenceInput is a that module covers sequence input into
+ Cinema via files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FileSequenceInputParserExceptionHandler.html">FileSequenceInputParserExceptionHandler</A></B></TD>
+<TD>FileSequenceInputParserExceptionHandler handles parser exceptions
+ to do with parsing files, and will display a dialog box.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FileSequenceOutput.html">FileSequenceOutput</A></B></TD>
+<TD>FileSequenceOutput is a module that covers sequence output to a
+ file from Cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FileSequenceParserExceptionHandler.html">FileSequenceParserExceptionHandler</A></B></TD>
+<TD>FileSequenceParserExceptionHandler handles parser exceptions
+ to do with parsing files, and will display a dialog box.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceInputModuleIdentifier.html">SequenceInputModuleIdentifier</A></B></TD>
+<TD>A module interface identifier for sequence input.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceOutputModuleIdentifier.html">SequenceOutputModuleIdentifier</A></B></TD>
+<TD>SequenceOutputModuleIdentifier.java
+
+
+ Created: Fri Aug 11 15:06:07 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-tree.html
new file mode 100644
index 0000000..220d4e3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/io/package-tree.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.io Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.io Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.io
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html"><B>CinemaCommandLineParserIdentifier</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.html"><B>SequenceInputModuleIdentifier</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/ [...]
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html"><B>AbstractSequenceInputParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.html"><B>FileSequenceInputParserExceptionHandler</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html"><B>AbstractSequenceParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.html"><B>FileSequenceParserExceptionHandler</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.html"><B>CinemaCommandLineParser</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.html"><B>AbstractSequenceInput</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.html"><B>FileSequenceInput</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.html"><B>AbstractSequenceOutput</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.io.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.html"><B>FileSequenceOutput</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html
new file mode 100644
index 0000000..73c5bf4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html
@@ -0,0 +1,582 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:32 BST 2002 -->
+<TITLE>
+CinemaMotifFrame
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaMotifFrame";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMotifFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.motif</FONT>
+<BR>
+Class CinemaMotifFrame</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">java.awt.Window</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">java.awt.Frame</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">javax.swing.JFrame</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaMotifFrame</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionListener. [...]
+
+<P>
+CinemaMotifFrame.java
+
+
+ Created: Tue Jan 16 13:54:41 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaMotifFrame.java,v 1.12 2001/07/10 14:15:24 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifFrame">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.AccessibleJFrame.html">JFrame.AccessibleJFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.AccessibleAWTFrame.html">Frame.AccessibleAWTFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.AccessibleAWTWindow.html">Window.AccessibleAWTWindow</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#EXIT_ON_CLOSE">EXIT_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPane">rootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPaneCheckingEnabled">rootPaneCheckingEnabled</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#CROSSHAIR_CURSOR">CROSSHAIR_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#DEFAULT_CURSOR">DEFAULT_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#E_RESIZE_CURSOR">E_RESIZE_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#HAND_CURSOR">HAND_CURSOR</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html">WindowConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DISPOSE_ON_CLOSE">DISPOSE_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DO_NOTHING_ON_CLOSE">DO_NOTHING_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#HIDE_ON_CLOSE">HIDE_ON_CLOSE</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#CinemaMotifFrame(uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel, uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule)">CinemaMotifFrame</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A> model,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#getCurrentlySelectedIndex()">getCurrentlySelectedIndex</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#getCurrentlySelectedName()">getCurrentlySelectedName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#getCurrentlySelectedRect()">getCurrentlySelectedRect</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#isCurrentlySelected()">isCurrentlySelected</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html#valueChanged(javax.swing.event.ListSelectionEvent)">valueChanged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionEvent.html">ListSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#createRootPane()">createRootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#frameInit()">frameInit</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#getAccessibleContext()">getAccessib [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getCursorType()">getCursorType</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getExtendedState()">getExtendedState</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addWindowFocusListener(java.awt.event.WindowFocusL [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#getFont()">getFont</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#postEvent(java.awt.Event)">postEvent</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaMotifFrame(uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel, uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule)"><!-- --></A><H3>
+CinemaMotifFrame</H3>
+<PRE>
+public <B>CinemaMotifFrame</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A> model,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html">CinemaMotifModule</A> module)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isCurrentlySelected()"><!-- --></A><H3>
+isCurrentlySelected</H3>
+<PRE>
+public boolean <B>isCurrentlySelected</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentlySelectedIndex()"><!-- --></A><H3>
+getCurrentlySelectedIndex</H3>
+<PRE>
+public int <B>getCurrentlySelectedIndex</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentlySelectedName()"><!-- --></A><H3>
+getCurrentlySelectedName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getCurrentlySelectedName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentlySelectedRect()"><!-- --></A><H3>
+getCurrentlySelectedRect</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getCurrentlySelectedRect</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="valueChanged(javax.swing.event.ListSelectionEvent)"><!-- --></A><H3>
+valueChanged</H3>
+<PRE>
+public void <B>valueChanged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionEvent.html">ListSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>valueChanged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ListSelectionListener.html">ListSelectionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><!-- --></A><H3>
+valueChanged</H3>
+<PRE>
+public void <B>valueChanged</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMotifFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html
new file mode 100644
index 0000000..e91cf4d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:33 BST 2002 -->
+<TITLE>
+CinemaMotifIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaMotifIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMotifIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.motif</FONT>
+<BR>
+Class CinemaMotifIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaMotifIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaMotifIdentifier.java
+
+
+ Created: Mon Jan 15 15:16:05 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaMotifIdentifier.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html">CinemaMotifIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html#CINEMA_MOTIF">CINEMA_MOTIF</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_MOTIF"><!-- --></A><H3>
+CINEMA_MOTIF</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html">CinemaMotifIdentifier</A> <B>CINEMA_MOTIF</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMotifIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html
new file mode 100644
index 0000000..346f84f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html
@@ -0,0 +1,373 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+CinemaMotifModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaMotifModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMotifModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.motif</FONT>
+<BR>
+Class CinemaMotifModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaMotifModule</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></DL>
+
+<P>
+CinemaMotifModule.java
+
+ This module is designed to handle motif selection and viewing
+ within Cinema.
+
+ Created: Wed Dec 27 14:57:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaMotifModule.java,v 1.5 2001/05/29 13:06:07 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#CinemaMotifModule()">CinemaMotifModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#getActions()">getActions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaMotifModule()"><!-- --></A><H3>
+CinemaMotifModule</H3>
+<PRE>
+public <B>CinemaMotifModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getActions()"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html#getActions()">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMotifModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html
new file mode 100644
index 0000000..48a94e0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html
@@ -0,0 +1,753 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+NamedAlignmentSelectionModel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NamedAlignmentSelectionModel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NamedAlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.motif</FONT>
+<BR>
+Class NamedAlignmentSelectionModel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.motif.NamedAlignmentSelectionModel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NamedAlignmentSelectionModel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A></DL>
+
+<P>
+NamedAlignmentSelectionModel.java
+
+ Stores multiple selections each one with a name.
+
+ Created: Wed Dec 27 15:20:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NamedAlignmentSelectionModel.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#NamedAlignmentSelectionModel()">NamedAlignmentSelectionModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#clearAllSelections()">clearAllSelections</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#clearSelection()">clearSelection</A></B>()</CODE>
+
+<BR>
+ Clear all the selections in this model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#clearSelection(java.lang.String)">clearSelection</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Start a selection at the given point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></B>()</CODE>
+
+<BR>
+ Returns the current selection or null if there is no
+ selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getCurrentSelectionName()">getCurrentSelectionName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></B>()</CODE>
+
+<BR>
+ Get the number of selections.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get the first selection rectangle which surrounds the point, or
+ null if there is not one.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get all selection rectangles which surround this point, or null
+ if there is not one</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></B>(int index)</CODE>
+
+<BR>
+ Gets the given selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getSelectionForName(java.lang.String)">getSelectionForName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#getSelectionNameIterator()">getSelectionNameIterator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Is the point within one of the selection rectangles</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#isSelecting()">isSelecting</A></B>()</CODE>
+
+<BR>
+ is the current selection in the process of being selected.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#resizeSelection(java.lang.String, uk.ac.man.bioinf.util.Direction, int)">resizeSelection</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> selection,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A> dir,
+ int size)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#setNameForSelection(java.lang.String, java.lang.String)">setNameForSelection</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> oldName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> newName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#sortMotifs()">sortMotifs</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Complete the selection at the given point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NamedAlignmentSelectionModel()"><!-- --></A><H3>
+NamedAlignmentSelectionModel</H3>
+<PRE>
+public <B>NamedAlignmentSelectionModel</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="sortMotifs()"><!-- --></A><H3>
+sortMotifs</H3>
+<PRE>
+public void <B>sortMotifs</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionNameIterator()"><!-- --></A><H3>
+getSelectionNameIterator</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A> <B>getSelectionNameIterator</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentSelectionName()"><!-- --></A><H3>
+getCurrentSelectionName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getCurrentSelectionName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionForName(java.lang.String)"><!-- --></A><H3>
+getSelectionForName</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSelectionForName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setNameForSelection(java.lang.String, java.lang.String)"><!-- --></A><H3>
+setNameForSelection</H3>
+<PRE>
+public void <B>setNameForSelection</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> oldName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> newName)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearAllSelections()"><!-- --></A><H3>
+clearAllSelections</H3>
+<PRE>
+public void <B>clearAllSelections</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection(java.lang.String)"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resizeSelection(java.lang.String, uk.ac.man.bioinf.util.Direction, int)"><!-- --></A><H3>
+resizeSelection</H3>
+<PRE>
+public void <B>resizeSelection</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> selection,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A> dir,
+ int size)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isSelecting()"><!-- --></A><H3>
+isSelecting</H3>
+<PRE>
+public boolean <B>isSelecting</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>is the current selection in the process of being selected.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isSelecting()">isSelecting</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>true is selection is changing</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentSelection()"><!-- --></A><H3>
+getCurrentSelection</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getCurrentSelection</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Returns the current selection or null if there is no
+ selection. If there is more than one selection this should return
+ the most recently made selection
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSelections()"><!-- --></A><H3>
+getNumberSelections</H3>
+<PRE>
+public int <B>getNumberSelections</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get the number of selections.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of selections</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionAt(int)"><!-- --></A><H3>
+getSelectionAt</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSelectionAt</B>(int index)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IndexOutOfBoundsException.html">IndexOutOfBoundsException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Gets the given selection. The index should reflect the
+ chronological order in which the selections were made, with the
+ smallest index first
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index
+<DT><B>Returns:</B><DD>the selection array index at the given index
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IndexOutOfBoundsException.html">IndexOutOfBoundsException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+isPointSelected</H3>
+<PRE>
+public boolean <B>isPointSelected</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Is the point within one of the selection rectangles
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point
+<DT><B>Returns:</B><DD>true if point is within a rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection()"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Clear all the selections in this model
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#clearSelection()">clearSelection</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectanglesAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[] <B>getRectanglesAtPoint</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get all selection rectangles which surround this point, or null
+ if there is not one
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangles surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectangleAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getRectangleAtPoint</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get the first selection rectangle which surrounds the point, or
+ null if there is not one.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangle surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+extendSelection</H3>
+<PRE>
+public void <B>extendSelection</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Start a selection at the given point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the start of the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+stopSelection</H3>
+<PRE>
+public void <B>stopSelection</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Complete the selection at the given point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point to complete the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+addAlignmentSelectionListener</H3>
+<PRE>
+public void <B>addAlignmentSelectionListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+removeAlignmentSelectionListener</H3>
+<PRE>
+public void <B>removeAlignmentSelectionListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><!-- --></A><H3>
+valueChanged</H3>
+<PRE>
+public void <B>valueChanged</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NamedAlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-frame.html
new file mode 100644
index 0000000..0556329
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-frame.html
@@ -0,0 +1,38 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.motif()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.motif()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.motif</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaMotifFrame.html" TARGET="classFrame">CinemaMotifFrame</A>
+<BR>
+<A HREF="CinemaMotifIdentifier.html" TARGET="classFrame">CinemaMotifIdentifier</A>
+<BR>
+<A HREF="CinemaMotifModule.html" TARGET="classFrame">CinemaMotifModule</A>
+<BR>
+<A HREF="NamedAlignmentSelectionModel.html" TARGET="classFrame">NamedAlignmentSelectionModel</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-summary.html
new file mode 100644
index 0000000..1bc20cc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-summary.html
@@ -0,0 +1,157 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.motif()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.motif()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.motif
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaMotifFrame.html">CinemaMotifFrame</A></B></TD>
+<TD>CinemaMotifFrame.java
+
+
+ Created: Tue Jan 16 13:54:41 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaMotifIdentifier.html">CinemaMotifIdentifier</A></B></TD>
+<TD>CinemaMotifIdentifier.java
+
+
+ Created: Mon Jan 15 15:16:05 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaMotifModule.html">CinemaMotifModule</A></B></TD>
+<TD>CinemaMotifModule.java
+
+ This module is designed to handle motif selection and viewing
+ within Cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A></B></TD>
+<TD>NamedAlignmentSelectionModel.java
+
+ Stores multiple selections each one with a name.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-tree.html
new file mode 100644
index 0000000..bab9702
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/motif/package-tree.html
@@ -0,0 +1,161 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.motif Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.motif Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.motif
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.html"><B>CinemaMotifIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html"><B>CinemaMotifFrame</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, javax.swing.even [...]
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.html"><B>CinemaMotifModule</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.html">CinemaActionProvider</A>)
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.motif.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html"><B>NamedAlignmentSelectionModel</B></A> (implements uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">Al [...]
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/io/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-frame.html
new file mode 100644
index 0000000..aaf4efe
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-frame.html
@@ -0,0 +1,48 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Cinema.html" TARGET="classFrame">Cinema</A>
+<BR>
+<A HREF="CinemaBoot.html" TARGET="classFrame">CinemaBoot</A>
+<BR>
+<A HREF="CinemaBootIdentifier.html" TARGET="classFrame">CinemaBootIdentifier</A>
+<BR>
+<A HREF="CinemaGuiModule.html" TARGET="classFrame">CinemaGuiModule</A>
+<BR>
+<A HREF="CinemaModule.html" TARGET="classFrame">CinemaModule</A>
+<BR>
+<A HREF="CinemaModuleFactoryInstance.html" TARGET="classFrame">CinemaModuleFactoryInstance</A>
+<BR>
+<A HREF="CinemaProperties.html" TARGET="classFrame">CinemaProperties</A>
+<BR>
+<A HREF="CinemaShared.html" TARGET="classFrame">CinemaShared</A>
+<BR>
+<A HREF="CinemaXMLParserFactory.html" TARGET="classFrame">CinemaXMLParserFactory</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-summary.html
new file mode 100644
index 0000000..61f6d63
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-summary.html
@@ -0,0 +1,191 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Cinema.html">Cinema</A></B></TD>
+<TD>Cinema.java
+
+
+ Created: Fri May 26 22:04:20 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaBoot.html">CinemaBoot</A></B></TD>
+<TD>CinemaBoot.java
+
+
+ Created: Mon May 29 17:58:12 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaBootIdentifier.html">CinemaBootIdentifier</A></B></TD>
+<TD>CinemaBootIdentifier.java
+
+
+ Created: Mon May 29 18:09:22 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+<TD>CinemaGuiModule.java
+
+
+ Created: Fri May 26 21:04:15 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaModule.html">CinemaModule</A></B></TD>
+<TD>CinemaModule.java
+
+ Most modules for Cinema should extend this interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaModuleFactoryInstance.html">CinemaModuleFactoryInstance</A></B></TD>
+<TD>CinemaModuleFactoryInstance.java
+
+ This class adds some reporting functions to the superclass.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaProperties.html">CinemaProperties</A></B></TD>
+<TD>CinemaProperties.java
+
+ This are all of the property names that the CinemaModule signals
+ changes for.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaShared.html">CinemaShared</A></B></TD>
+<TD>CinemaShared.java
+
+
+ Created: Tue Sep 12 17:22:26 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaXMLParserFactory.html">CinemaXMLParserFactory</A></B></TD>
+<TD>CinemaXMLParserFactory.java
+
+
+ Created: Mon Sep 18 18:59:17 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-tree.html
new file mode 100644
index 0000000..6e26441
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/package-tree.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html"><B>CinemaBootIdentifier</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html"><B>CinemaProperties</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/Cinema.html"><B>Cinema</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html"><B>CinemaXMLParserFactory</B></A> (implements uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>DefaultModuleFactoryInstance</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html"><B>CinemaModuleFactoryInstance</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>XMLBootModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html"><B>CinemaBoot</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaShared.html"><B>CinemaShared</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/analysis/regexp/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/color/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html
new file mode 100644
index 0000000..8db0b90
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html
@@ -0,0 +1,372 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+CinemaResources
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaResources";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaResources.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.resources</FONT>
+<BR>
+Class CinemaResources</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.resources.CinemaResources</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaResources</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CinemaResources.java
+
+ The purpose of this class is to provide access to the resources
+ that cinema needs in a manner which is appropriate and simple both
+ during development time and after deployment.
+
+
+ Created: Mon May 29 16:44:01 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaResources.java,v 1.9 2001/05/04 12:30:33 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#CinemaResources()">CinemaResources</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#fetchCinemaDirectoryString()">fetchCinemaDirectoryString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#fetchModuleSystemIdentifier()">fetchModuleSystemIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getModuleDTDAsResource()">getModuleDTDAsResource</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getResource(java.lang.String)">getResource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getUserExtensions()">getUserExtensions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#getUserPersist()">getUserPersist</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html#resolveXMLLoadName(java.lang.String)">resolveXMLLoadName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> loadName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaResources()"><!-- --></A><H3>
+CinemaResources</H3>
+<PRE>
+public <B>CinemaResources</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getResource(java.lang.String)"><!-- --></A><H3>
+getResource</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getResource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUserExtensions()"><!-- --></A><H3>
+getUserExtensions</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> <B>getUserExtensions</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUserPersist()"><!-- --></A><H3>
+getUserPersist</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> <B>getUserPersist</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveXMLLoadName(java.lang.String)"><!-- --></A><H3>
+resolveXMLLoadName</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>resolveXMLLoadName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> loadName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModuleDTDAsResource()"><!-- --></A><H3>
+getModuleDTDAsResource</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>getModuleDTDAsResource</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fetchModuleSystemIdentifier()"><!-- --></A><H3>
+fetchModuleSystemIdentifier</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchModuleSystemIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fetchCinemaDirectoryString()"><!-- --></A><H3>
+fetchCinemaDirectoryString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchCinemaDirectoryString</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaResources.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-frame.html
new file mode 100644
index 0000000..38006be
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-frame.html
@@ -0,0 +1,32 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.resources()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.resources()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.resources</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaResources.html" TARGET="classFrame">CinemaResources</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-summary.html
new file mode 100644
index 0000000..234cc38
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-summary.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.resources()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.resources()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.resources
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaResources.html">CinemaResources</A></B></TD>
+<TD>CinemaResources.java
+
+ The purpose of this class is to provide access to the resources
+ that cinema needs in a manner which is appropriate and simple both
+ during development time and after deployment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-tree.html
new file mode 100644
index 0000000..159dea7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/resources/package-tree.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.resources Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.resources Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.resources
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.resources.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.html"><B>CinemaResources</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html
new file mode 100644
index 0000000..a18ff3c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html
@@ -0,0 +1,285 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+CinemaDebug.DebugImpl
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaDebug.DebugImpl";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.DebugImpl.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.shared</FONT>
+<BR>
+Class CinemaDebug.DebugImpl</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">uk.ac.man.bioinf.debug.AbstractDebug</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug.DebugImpl</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaDebug.DebugImpl</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html#CinemaDebug.DebugImpl()">CinemaDebug.DebugImpl</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.debug.AbstractDebug"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.debug.<A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/de [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaDebug.DebugImpl()"><!-- --></A><H3>
+CinemaDebug.DebugImpl</H3>
+<PRE>
+public <B>CinemaDebug.DebugImpl</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in class <CODE><A HREF="../../../.. [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in class <CODE><A HRE [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.DebugImpl.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html
new file mode 100644
index 0000000..1a1668b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html
@@ -0,0 +1,394 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+CinemaDebug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaDebug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.shared</FONT>
+<BR>
+Class CinemaDebug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.shared.CinemaDebug</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaDebug</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></DL>
+
+<P>
+CinemaDebug.java
+
+ This class provides the Debugging architecture implementation for
+ Cinema. It provides a Console GUI, files logs and oh so much more...
+
+ Eventually the initial state of this should result from the XML
+ initiation, but at the moment it just does lots of things at once.
+
+ Created: Sun May 7 18:36:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaDebug.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#CinemaDebug()">CinemaDebug</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Mo [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaDebug()"><!-- --></A><H3>
+CinemaDebug</H3>
+<PRE>
+public <B>CinemaDebug</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html
new file mode 100644
index 0000000..32b36a1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html
@@ -0,0 +1,310 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+CinemaSharedIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaSharedIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSharedIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.shared</FONT>
+<BR>
+Class CinemaSharedIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaSharedIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaSharedIdentifier.java
+
+
+ Created: Fri Sep 15 13:45:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaSharedIdentifier.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html#CINEMA_DEBUG">CINEMA_DEBUG</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html#CINEMA_QUIT_EXIT">CINEMA_QUIT_EXIT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html#CINEMA_SPLASH">CINEMA_SPLASH</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_SPLASH"><!-- --></A><H3>
+CINEMA_SPLASH</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A> <B>CINEMA_SPLASH</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_DEBUG"><!-- --></A><H3>
+CINEMA_DEBUG</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A> <B>CINEMA_DEBUG</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_QUIT_EXIT"><!-- --></A><H3>
+CINEMA_QUIT_EXIT</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html">CinemaSharedIdentifier</A> <B>CINEMA_QUIT_EXIT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSharedIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html
new file mode 100644
index 0000000..ffc9ee8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html
@@ -0,0 +1,289 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:34 BST 2002 -->
+<TITLE>
+CinemaSharedQuitExit
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaSharedQuitExit";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSharedQuitExit.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.shared</FONT>
+<BR>
+Class CinemaSharedQuitExit</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaSharedQuitExit</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></DL>
+
+<P>
+CinemaSharedQuitExit.java
+
+
+ Created: Fri Sep 15 13:51:24 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaSharedQuitExit.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html#CinemaSharedQuitExit()">CinemaSharedQuitExit</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html#getActions(uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui)">getActions</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A> gui)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Mo [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaSharedQuitExit()"><!-- --></A><H3>
+CinemaSharedQuitExit</H3>
+<PRE>
+public <B>CinemaSharedQuitExit</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getActions(uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui)"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A> gui)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSharedQuitExit.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html
new file mode 100644
index 0000000..69258ed
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html
@@ -0,0 +1,341 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:35 BST 2002 -->
+<TITLE>
+CinemaSplash
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaSplash";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSplash.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.shared</FONT>
+<BR>
+Class CinemaSplash</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaSplash</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaSplash.java
+
+
+ Created: Tue Dec 12 17:42:27 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaSplash.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#CinemaSplash()">CinemaSplash</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#killSplash()">killSplash</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaSplash()"><!-- --></A><H3>
+CinemaSplash</H3>
+<PRE>
+public <B>CinemaSplash</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="killSplash()"><!-- --></A><H3>
+killSplash</H3>
+<PRE>
+public void <B>killSplash</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSplash.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-frame.html
new file mode 100644
index 0000000..86fac1b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-frame.html
@@ -0,0 +1,38 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:09 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.shared()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.shared()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.shared</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaDebug.html" TARGET="classFrame">CinemaDebug</A>
+<BR>
+<A HREF="CinemaSharedIdentifier.html" TARGET="classFrame">CinemaSharedIdentifier</A>
+<BR>
+<A HREF="CinemaSharedQuitExit.html" TARGET="classFrame">CinemaSharedQuitExit</A>
+<BR>
+<A HREF="CinemaSplash.html" TARGET="classFrame">CinemaSplash</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-summary.html
new file mode 100644
index 0000000..bab5099
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-summary.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.shared()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.shared()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.shared
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaDebug.html">CinemaDebug</A></B></TD>
+<TD>CinemaDebug.java
+
+ This class provides the Debugging architecture implementation for
+ Cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaSharedIdentifier.html">CinemaSharedIdentifier</A></B></TD>
+<TD>CinemaSharedIdentifier.java
+
+
+ Created: Fri Sep 15 13:45:25 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaSharedQuitExit.html">CinemaSharedQuitExit</A></B></TD>
+<TD>CinemaSharedQuitExit.java
+
+
+ Created: Fri Sep 15 13:51:24 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaSplash.html">CinemaSplash</A></B></TD>
+<TD>CinemaSplash.java
+
+
+ Created: Tue Dec 12 17:42:27 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-tree.html
new file mode 100644
index 0000000..7d9827a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/shared/package-tree.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.shared Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.shared Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.shared
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html"><B>AbstractDebug</B></A> (implements uk.ac.man.bioinf.debug.<A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html"><B>CinemaDebug.DebugImpl</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.html"><B>CinemaSharedIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html"><B>CinemaDebug</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.html"><B>CinemaSharedQuitExit</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.shared.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.html"><B>CinemaSplash</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/resources/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html
new file mode 100644
index 0000000..9ce97f1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html
@@ -0,0 +1,708 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:28 BST 2002 -->
+<TITLE>
+CinemaAlignmentFrame
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaAlignmentFrame";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaAlignmentFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaAlignmentFrame</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">java.awt.Window</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">java.awt.Frame</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">javax.swing.JFrame</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">uk.ac.man.bioinf.gui.optionable.OptionableJFrame</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="../../../../../. [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaAlignmentFrame</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DL>
+
+<P>
+CinemaAlignmentFrame.java
+
+ This class provides a basic CinemaAlignmentFrame which consists of
+ a JScrollPane, with an JAlignmentViewer in the middle,
+ JAlignmentButton panel down the right hand side and a
+ JAlignmentRuler across the bottom.
+
+ Created: Tue Jun 20 15:01:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaAlignmentFrame.java,v 1.12 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.AccessibleJFrame.html">JFrame.AccessibleJFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.AccessibleAWTFrame.html">Frame.AccessibleAWTFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.AccessibleAWTWindow.html">Window.AccessibleAWTWindow</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#EXIT_ON_CLOSE">EXIT_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPane">rootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPaneCheckingEnabled">rootPaneCheckingEnabled</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#CROSSHAIR_CURSOR">CROSSHAIR_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#DEFAULT_CURSOR">DEFAULT_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#E_RESIZE_CURSOR">E_RESIZE_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#HAND_CURSOR">HAND_CURSOR</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html">WindowConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DISPOSE_ON_CLOSE">DISPOSE_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DO_NOTHING_ON_CLOSE">DO_NOTHING_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#HIDE_ON_CLOSE">HIDE_ON_CLOSE</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#CinemaAlignmentFrame(java.lang.String, java.lang.String)">CinemaAlignmentFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#CinemaAlignmentFrame(java.lang.String, java.lang.String, boolean)">CinemaAlignmentFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ boolean delayOptionable)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#CinemaAlignmentFrame(java.lang.String, java.lang.String, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">CinemaAlignmentFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#dispose()">dispose</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getMainPanel()">getMainPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getOptions()">getOptions</A></B>()</CODE>
+
+<BR>
+ An implementation of the Optionable interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getRowHeaders()">getRowHeaders</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getRuler()">getRuler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getRulerPanel()">getRulerPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getScrollPane()">getScrollPane</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#getViewer()">getViewer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#setOptions(java.lang.Object)">setOptions</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> opts)</CODE>
+
+<BR>
+ Implementation of the Optionable Interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.optionable.OptionableJFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#defaultPack()">defaultPack</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#forceOptionable()">forceOptionable</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getDefaultOptionHandler()">getDefaultOptionHandler</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptionGroupName [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#createRootPane()">createRootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#frameInit()">frameInit</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#getAccessibleContext()">getAccessib [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getCursorType()">getCursorType</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getExtendedState()">getExtendedState</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addWindowFocusListener(java.awt.event.WindowFocusL [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#getFont()">getFont</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#postEvent(java.awt.Event)">postEvent</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaAlignmentFrame(java.lang.String, java.lang.String, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+CinemaAlignmentFrame</H3>
+<PRE>
+public <B>CinemaAlignmentFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="CinemaAlignmentFrame(java.lang.String, java.lang.String)"><!-- --></A><H3>
+CinemaAlignmentFrame</H3>
+<PRE>
+public <B>CinemaAlignmentFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="CinemaAlignmentFrame(java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>
+CinemaAlignmentFrame</H3>
+<PRE>
+public <B>CinemaAlignmentFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ boolean delayOptionable)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setSequenceAlignment</H3>
+<PRE>
+public void <B>setSequenceAlignment</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMainPanel()"><!-- --></A><H3>
+getMainPanel</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>getMainPanel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRowHeaders()"><!-- --></A><H3>
+getRowHeaders</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A> <B>getRowHeaders</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollPane()"><!-- --></A><H3>
+getScrollPane</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A> <B>getScrollPane</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRulerPanel()"><!-- --></A><H3>
+getRulerPanel</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A> <B>getRulerPanel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getViewer()"><!-- --></A><H3>
+getViewer</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>getViewer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRuler()"><!-- --></A><H3>
+getRuler</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html">JAlignmentRuler</A> <B>getRuler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptions(java.lang.Object)"><!-- --></A><H3>
+setOptions</H3>
+<PRE>
+public void <B>setOptions</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> opts)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A></CODE></B></DD>
+<DD>Implementation of the Optionable Interface.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)">setOptions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptions(java.lang.Object)">setOptions</A></CODE> in class <CODE><A HREF="../../../../../. [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>opts</CODE> - <DT><B>See Also:</B><DD><CODE>getOptions</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptions()"><!-- --></A><H3>
+getOptions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getOptions</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A></CODE></B></DD>
+<DD>An implementation of the Optionable interface. Subclasses overriding this method
+ should call super.getOptions. Also the constructor documentation and the delayOptionable
+ parameter should be considered.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptions()">getOptions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptions()">getOptions</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/option [...]
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the options</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="dispose()"><!-- --></A><H3>
+dispose</H3>
+<PRE>
+public void <B>dispose</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#dispose()">dispose</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaAlignmentFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html
new file mode 100644
index 0000000..d148586
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html
@@ -0,0 +1,285 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:30 BST 2002 -->
+<TITLE>
+CinemaDebug.DebugImpl
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaDebug.DebugImpl";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.DebugImpl.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaDebug.DebugImpl</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">uk.ac.man.bioinf.debug.AbstractDebug</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug.DebugImpl</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaDebug.DebugImpl</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html#CinemaDebug.DebugImpl()">CinemaDebug.DebugImpl</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.debug.AbstractDebug"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.debug.<A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/de [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaDebug.DebugImpl()"><!-- --></A><H3>
+CinemaDebug.DebugImpl</H3>
+<PRE>
+public <B>CinemaDebug.DebugImpl</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in class <CODE><A HREF="../../../.. [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in class <CODE><A HRE [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.DebugImpl.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html
new file mode 100644
index 0000000..8478ff6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html
@@ -0,0 +1,394 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:30 BST 2002 -->
+<TITLE>
+CinemaDebug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaDebug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaDebug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaDebug</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></DL>
+
+<P>
+CinemaDebug.java
+
+ This class provides the Debugging architecture implementation for
+ Cinema. It provides a Console GUI, files logs and oh so much more...
+
+ Eventually the initial state of this should result from the XML
+ initiation, but at the moment it just does lots of things at once.
+
+ Created: Sun May 7 18:36:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaDebug.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#CinemaDebug()">CinemaDebug</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Mo [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaDebug()"><!-- --></A><H3>
+CinemaDebug</H3>
+<PRE>
+public <B>CinemaDebug</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html
new file mode 100644
index 0000000..19200c5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html
@@ -0,0 +1,398 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:30 BST 2002 -->
+<TITLE>
+CinemaFileOptionableExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaFileOptionableExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaFileOptionableExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaFileOptionableExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaFileOptionableExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaFileOptionableExceptionHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></DL>
+
+<P>
+CinemaFileOptionableExceptionHandler.java
+
+
+ Created: Mon May 14 16:21:58 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaFileOptionableExceptionHandler.java,v 1.2 2001/05/15 12:24:15 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#CinemaFileOptionableExceptionHandler()">CinemaFileOptionableExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(java.lang.ClassNotFoundException)">handleLoadException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ClassNotFoundException.html">ClassNotFoundException</A> exp)</CODE>
+
+<BR>
+ ClassNotFoundException can occur when reading data from the
+ stream for a data type that does not exist.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(java.lang.Exception)">handleLoadException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</CODE>
+
+<BR>
+ Handle an exception occurring during the loading of options.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(java.io.IOException)">handleLoadException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> ioe)</CODE>
+
+<BR>
+ Signalled if some unknown IOException occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)">handleLoadException</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A> osnfe)</CODE>
+
+<BR>
+ If the optionable load file can not be found this error is signalled.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleSaveException(java.lang.Exception)">handleSaveException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</CODE>
+
+<BR>
+ If something nasty occurs whilst gather the optionable
+ information occurs this is error is signalled.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html#handleSaveException(java.io.IOException)">handleSaveException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> iop)</CODE>
+
+<BR>
+ If the save encounters IO problems!</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaFileOptionableExceptionHandler()"><!-- --></A><H3>
+CinemaFileOptionableExceptionHandler</H3>
+<PRE>
+public <B>CinemaFileOptionableExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleLoadException(java.lang.Exception)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></B></DD>
+<DD>Handle an exception occurring during the loading of options.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.lang.Exception)">handleLoadException</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> -
+<DT><B>Returns:</B><DD>true if the an attempt should be made to load the options
+ again.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleLoadException(java.io.IOException)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> ioe)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></B></DD>
+<DD>Signalled if some unknown IOException occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.io.IOException)">handleLoadException</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>ioe</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleLoadException(java.lang.ClassNotFoundException)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ClassNotFoundException.html">ClassNotFoundException</A> exp)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></B></DD>
+<DD>ClassNotFoundException can occur when reading data from the
+ stream for a data type that does not exist. It won't normally
+ occur.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.lang.ClassNotFoundException)">handleLoadException</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A> osnfe)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></B></DD>
+<DD>If the optionable load file can not be found this error is signalled.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)">handleLoadException</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>osnfe</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleSaveException(java.lang.Exception)"><!-- --></A><H3>
+handleSaveException</H3>
+<PRE>
+public boolean <B>handleSaveException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></B></DD>
+<DD>If something nasty occurs whilst gather the optionable
+ information occurs this is error is signalled.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleSaveException(java.lang.Exception)">handleSaveException</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleSaveException(java.io.IOException)"><!-- --></A><H3>
+handleSaveException</H3>
+<PRE>
+public boolean <B>handleSaveException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> iop)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></B></DD>
+<DD>If the save encounters IO problems!
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleSaveException(java.io.IOException)">handleSaveException</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>iop</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaFileOptionableExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html
new file mode 100644
index 0000000..13c91eb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html
@@ -0,0 +1,373 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:30 BST 2002 -->
+<TITLE>
+CinemaFilePersist
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaFilePersist";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaFilePersist.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaFilePersist</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaFilePersist</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A></DL>
+
+<P>
+CinemaFilePersist.java
+
+
+ Created: Tue Jan 30 15:53:21 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaFilePersist.java,v 1.4 2001/05/14 17:08:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#CinemaFilePersist()">CinemaFilePersist</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#getOptionHandler()">getOptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaFilePersist()"><!-- --></A><H3>
+CinemaFilePersist</H3>
+<PRE>
+public <B>CinemaFilePersist</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionHandler()"><!-- --></A><H3>
+getOptionHandler</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getOptionHandler</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#getOptionHandler()">getOptionHandler</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html">CinemaPersist</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaFilePersist.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html
new file mode 100644
index 0000000..662e0c6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html
@@ -0,0 +1,362 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:30 BST 2002 -->
+<TITLE>
+CinemaInvoker
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaInvoker";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaInvoker.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaInvoker</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CinemaInvoker</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></DL>
+
+<P>
+CinemaInvoker.java
+
+
+ Created: Tue Apr 25 20:24:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaInvoker.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#CinemaInvoker()">CinemaInvoker</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getInvokerInternalQueue()">getInvokerInternalQueue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getNewInvokerInternalQueue()">getNewInvokerInternalQueue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Mo [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaInvoker()"><!-- --></A><H3>
+CinemaInvoker</H3>
+<PRE>
+public <B>CinemaInvoker</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInvokerInternalQueue()"><!-- --></A><H3>
+getInvokerInternalQueue</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> <B>getInvokerInternalQueue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNewInvokerInternalQueue()"><!-- --></A><H3>
+getNewInvokerInternalQueue</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> <B>getNewInvokerInternalQueue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaInvoker.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html
new file mode 100644
index 0000000..2378796
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html
@@ -0,0 +1,358 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:31 BST 2002 -->
+<TITLE>
+CinemaMenuBuilder
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaMenuBuilder";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMenuBuilder.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaMenuBuilder</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaMenuBuilder</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaMenuBuilder.java
+
+ This class builds a menu system based upon the module configuration
+ information.
+ The format of the config info should look something like this...
+
+ <code>
+ <pre>
+ <!-- The File Menu -->
+
+ <node>
+ <value>File</value>
+ <node>
+ <!-- Provides the open alignment -->
+ <name>SEQ_INPUT</name>
+ </node>
+ <node>
+ <!-- Provides the save alignment -->
+ <name>SEQ_OUTPUT</name>
+ </node>
+ </node>
+
+ <!-- The Colour Selector -->
+ <node>
+ <value>Colour Selector</value>
+ <node>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ </node>
+ </node>
+ </node>
+ </pre>
+ </code>
+
+ Essentially a "Value" is translated as the title of a menu whilst
+ "name" is translated as a Module which will provide actions for
+ that menu. This makes arbitrarily deep menu systems to be
+ constructed.
+
+ Created: Fri Oct 13 15:26:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaMenuBuilder.java,v 1.5 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html#CinemaMenuBuilder()">CinemaMenuBuilder</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html#buildMenu(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame, javax.swing.JMenuBar, uk.ac.man.bioinf.apps.xml.ConfigNode[])">buildMenu</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A> menuBar,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>[] mainMenuItems)</CODE>
+
+<BR>
+ This is the build method.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaMenuBuilder()"><!-- --></A><H3>
+CinemaMenuBuilder</H3>
+<PRE>
+public <B>CinemaMenuBuilder</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="buildMenu(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame, javax.swing.JMenuBar, uk.ac.man.bioinf.apps.xml.ConfigNode[])"><!-- --></A><H3>
+buildMenu</H3>
+<PRE>
+public void <B>buildMenu</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuBar.html">JMenuBar</A> menuBar,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>[] mainMenuItems)</PRE>
+<DL>
+<DD>This is the build method. The ConfigNode should be the root nodes
+ which describe the menu system.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>frame</CODE> - this is optional and can be null. If it is present
+ then it will be passed to those menu items which require it.<DD><CODE>menuBar</CODE> - this is the JMenuBar to use.<DD><CODE>mainMenuItems</CODE> - this are there configuration nodes which
+ describe the menu system.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMenuBuilder.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html
new file mode 100644
index 0000000..9f0d90a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html
@@ -0,0 +1,489 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:31 BST 2002 -->
+<TITLE>
+CinemaMultipleConsensusViewer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaMultipleConsensusViewer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMultipleConsensusViewer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaMultipleConsensusViewer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyCh [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaMultipleConsensusViewer</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></DL>
+
+<P>
+CinemaMultipleConsensusViewer.java
+
+
+ Created: Fri Jun 23 12:09:24 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaMultipleConsensusViewer.java,v 1.7 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#CinemaMultipleConsensusViewer()">CinemaMultipleConsensusViewer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#addConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)">addConsensusSequence</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ The method called, from an external source, to remove this module
+ and prepare it for garbage collection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> evt)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#removeConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)">removeConsensusSequence</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaMultipleConsensusViewer()"><!-- --></A><H3>
+CinemaMultipleConsensusViewer</H3>
+<PRE>
+public <B>CinemaMultipleConsensusViewer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><!-- --></A><H3>
+addConsensusSequence</H3>
+<PRE>
+public void <B>addConsensusSequence</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeConsensusSequence(uk.ac.man.bioinf.analysis.consensus.ConsensusSequence)"><!-- --></A><H3>
+removeConsensusSequence</H3>
+<PRE>
+public void <B>removeConsensusSequence</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A> sequence)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#destroy()">destroy</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> evt)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaMultipleConsensusViewer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html
new file mode 100644
index 0000000..dfc7f2a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html
@@ -0,0 +1,316 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:31 BST 2002 -->
+<TITLE>
+CinemaPersist
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaPersist";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaPersist.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaPersist</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html">CinemaFilePersist</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>CinemaPersist</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaPersist.java
+
+ Provides the OptionHandler which classes need to implement persistance.
+ Created: Tue Jan 30 15:31:24 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaPersist.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#CinemaPersist()">CinemaPersist</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#getOptionHandler()">getOptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaPersist()"><!-- --></A><H3>
+CinemaPersist</H3>
+<PRE>
+public <B>CinemaPersist</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionHandler()"><!-- --></A><H3>
+getOptionHandler</H3>
+<PRE>
+public abstract <A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getOptionHandler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaPersist.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html
new file mode 100644
index 0000000..e4f17f2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html
@@ -0,0 +1,318 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:31 BST 2002 -->
+<TITLE>
+CinemaRegexp
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaRegexp";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaRegexp.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaRegexp</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaRegexp</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></DL>
+
+<P>
+CinemaRegexp.java
+
+ Provides support for various regexp searching facilities.
+
+ Created: Fri Feb 9 11:38:52 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaRegexp.java,v 1.4 2001/05/22 16:03:01 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html#CinemaRegexp()">CinemaRegexp</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaRegexp()"><!-- --></A><H3>
+CinemaRegexp</H3>
+<PRE>
+public <B>CinemaRegexp</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaRegexp.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html
new file mode 100644
index 0000000..174b10e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html
@@ -0,0 +1,339 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:31 BST 2002 -->
+<TITLE>
+CinemaResizeElements
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaResizeElements";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaResizeElements.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaResizeElements</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaResizeElements</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></DL>
+
+<P>
+CinemaResizeElements.java
+
+
+ Created: Wed Jul 26 14:40:14 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaResizeElements.java,v 1.9 2001/07/06 12:51:58 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#CinemaResizeElements()">CinemaResizeElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaResizeElements()"><!-- --></A><H3>
+CinemaResizeElements</H3>
+<PRE>
+public <B>CinemaResizeElements</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)"><!-- --></A><H3>
+getActions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Action.html">Action</A>[] <B>getActions</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A> frame)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html#getActions(uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame)">getActions</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaResizeElements.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html
new file mode 100644
index 0000000..e1bfa40
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html
@@ -0,0 +1,325 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:31 BST 2002 -->
+<TITLE>
+CinemaSlaveViewerModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaSlaveViewerModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSlaveViewerModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaSlaveViewerModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaSlaveViewerModule</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DL>
+
+<P>
+CinemaSlaveViewerModule.java
+
+ Generates arbitrary numbers of Slave Viewers. At lot of the code
+ here is very similar to that in CinemaCoreGui, and it would
+ probably make sense to consolidate some of this into a single
+ place.
+
+ The point of a slave viewer is to show an alignment which is not
+ the main alignment. It will not produce events like the main
+ alignment, and will not control everything else. At the moment the
+ main reason for writing this is so that I can test out some other
+ data structures I have written but I think that this will be a
+ useful functionality in the end.
+
+ Created: Sun Jun 4 20:26:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaSlaveViewerModule.java,v 1.7 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html#CinemaSlaveViewerModule()">CinemaSlaveViewerModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html#showSlaveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">showSlaveAlignment</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaSlaveViewerModule()"><!-- --></A><H3>
+CinemaSlaveViewerModule</H3>
+<PRE>
+public <B>CinemaSlaveViewerModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="showSlaveAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+showSlaveAlignment</H3>
+<PRE>
+public void <B>showSlaveAlignment</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaSlaveViewerModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html
new file mode 100644
index 0000000..d5a1908
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html
@@ -0,0 +1,355 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:32 BST 2002 -->
+<TITLE>
+CinemaStatusInformation
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaStatusInformation";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaStatusInformation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaStatusInformation</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">uk.ac.man.bioinf.apps.xml.XMLModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">uk.ac.man.bioinf.apps.cinema.CinemaModule</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">uk.ac.man.bioinf.apps.cinema.CinemaGuiModule</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaStatusInformation</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DL>
+
+<P>
+CinemaStatusInformation.java
+
+ A utility class which provides what are hopefully useful status bar
+ information messages about what Cinema is currently showing.
+
+ Created: Fri Jan 26 15:49:33 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaStatusInformation.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#CinemaStatusInformation()">CinemaStatusInformation</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaGuiModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html">CinemaGuiModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getAlignmentFrame()">getAlignmentFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getFrame()">getFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html#getJMenuBar()">getJMenuBar</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.cinema.CinemaModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java.beans.PropertyChangeListener)">addCinemaPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html#addCinemaPropertyChangeListener(java. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.xml.XMLModule"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html">XMLModule</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CinemaStatusInformation()"><!-- --></A><H3>
+CinemaStatusInformation</H3>
+<PRE>
+public <B>CinemaStatusInformation</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaStatusInformation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html
new file mode 100644
index 0000000..5466236
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html
@@ -0,0 +1,418 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:32 BST 2002 -->
+<TITLE>
+CinemaUtilityIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CinemaUtilityIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaUtilityIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class CinemaUtilityIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CinemaUtilityIdentifier</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+CinemaUtilityIdentifier.java
+
+
+ Created: Thu May 25 14:27:34 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CinemaUtilityIdentifier.java,v 1.14 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_FILE_PERSIST">CINEMA_FILE_PERSIST</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_INVOKER">CINEMA_INVOKER</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_MENU_BUILDER">CINEMA_MENU_BUILDER</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_MULTIPLE_CONSENSUS">CINEMA_MULTIPLE_CONSENSUS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_PERSIST">CINEMA_PERSIST</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_REGEXP">CINEMA_REGEXP</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_RESIZE_ELEMENTS">CINEMA_RESIZE_ELEMENTS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_SLAVE_VIEWER">CINEMA_SLAVE_VIEWER</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html#CINEMA_STATUS">CINEMA_STATUS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumerate [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CINEMA_REGEXP"><!-- --></A><H3>
+CINEMA_REGEXP</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_REGEXP</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_STATUS"><!-- --></A><H3>
+CINEMA_STATUS</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_STATUS</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_MULTIPLE_CONSENSUS"><!-- --></A><H3>
+CINEMA_MULTIPLE_CONSENSUS</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_MULTIPLE_CONSENSUS</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_INVOKER"><!-- --></A><H3>
+CINEMA_INVOKER</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_INVOKER</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_SLAVE_VIEWER"><!-- --></A><H3>
+CINEMA_SLAVE_VIEWER</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_SLAVE_VIEWER</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_RESIZE_ELEMENTS"><!-- --></A><H3>
+CINEMA_RESIZE_ELEMENTS</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_RESIZE_ELEMENTS</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_MENU_BUILDER"><!-- --></A><H3>
+CINEMA_MENU_BUILDER</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_MENU_BUILDER</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_PERSIST"><!-- --></A><H3>
+CINEMA_PERSIST</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_PERSIST</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CINEMA_FILE_PERSIST"><!-- --></A><H3>
+CINEMA_FILE_PERSIST</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A> <B>CINEMA_FILE_PERSIST</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CinemaUtilityIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html
new file mode 100644
index 0000000..693fe71
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:32 BST 2002 -->
+<TITLE>
+ConsensusPercentageIDColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ConsensusPercentageIDColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusPercentageIDColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.cinema.utils</FONT>
+<BR>
+Class ConsensusPercentageIDColorMap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.cinema.utils.ConsensusPercentageIDColorMap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ConsensusPercentageIDColorMap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></DL>
+
+<P>
+ConsensusPercentageIDColorMap.java
+
+
+ Created: Fri Jun 23 17:57:45 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ConsensusPercentageIDColorMap.java,v 1.6 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#ConsensusPercentageIDColorMap(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">ConsensusPercentageIDColorMap</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the Color at a specific position in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this colour scheme.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ConsensusPercentageIDColorMap(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+ConsensusPercentageIDColorMap</H3>
+<PRE>
+public <B>ConsensusPercentageIDColorMap</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the Color at a specific position in the alignment. This
+ method will do various things depending on the actual color map
+ implemented.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>elem</CODE> - the element<DD><CODE>point</CODE> - the location within the SA
+<DT><B>Returns:</B><DD>the color</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the name of this colour scheme.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConsensusPercentageIDColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-frame.html
new file mode 100644
index 0000000..9ba16f8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-frame.html
@@ -0,0 +1,58 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.utils()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.utils()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.cinema.utils</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CinemaAlignmentFrame.html" TARGET="classFrame">CinemaAlignmentFrame</A>
+<BR>
+<A HREF="CinemaDebug.html" TARGET="classFrame">CinemaDebug</A>
+<BR>
+<A HREF="CinemaFileOptionableExceptionHandler.html" TARGET="classFrame">CinemaFileOptionableExceptionHandler</A>
+<BR>
+<A HREF="CinemaFilePersist.html" TARGET="classFrame">CinemaFilePersist</A>
+<BR>
+<A HREF="CinemaInvoker.html" TARGET="classFrame">CinemaInvoker</A>
+<BR>
+<A HREF="CinemaMenuBuilder.html" TARGET="classFrame">CinemaMenuBuilder</A>
+<BR>
+<A HREF="CinemaMultipleConsensusViewer.html" TARGET="classFrame">CinemaMultipleConsensusViewer</A>
+<BR>
+<A HREF="CinemaPersist.html" TARGET="classFrame">CinemaPersist</A>
+<BR>
+<A HREF="CinemaRegexp.html" TARGET="classFrame">CinemaRegexp</A>
+<BR>
+<A HREF="CinemaResizeElements.html" TARGET="classFrame">CinemaResizeElements</A>
+<BR>
+<A HREF="CinemaSlaveViewerModule.html" TARGET="classFrame">CinemaSlaveViewerModule</A>
+<BR>
+<A HREF="CinemaStatusInformation.html" TARGET="classFrame">CinemaStatusInformation</A>
+<BR>
+<A HREF="CinemaUtilityIdentifier.html" TARGET="classFrame">CinemaUtilityIdentifier</A>
+<BR>
+<A HREF="ConsensusPercentageIDColorMap.html" TARGET="classFrame">ConsensusPercentageIDColorMap</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-summary.html
new file mode 100644
index 0000000..a95da27
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-summary.html
@@ -0,0 +1,227 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.utils()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.utils()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/commandline/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.cinema.utils
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaAlignmentFrame.html">CinemaAlignmentFrame</A></B></TD>
+<TD>CinemaAlignmentFrame.java
+
+ This class provides a basic CinemaAlignmentFrame which consists of
+ a JScrollPane, with an JAlignmentViewer in the middle,
+ JAlignmentButton panel down the right hand side and a
+ JAlignmentRuler across the bottom.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaDebug.html">CinemaDebug</A></B></TD>
+<TD>CinemaDebug.java
+
+ This class provides the Debugging architecture implementation for
+ Cinema.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A></B></TD>
+<TD>CinemaFileOptionableExceptionHandler.java
+
+
+ Created: Mon May 14 16:21:58 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaFilePersist.html">CinemaFilePersist</A></B></TD>
+<TD>CinemaFilePersist.java
+
+
+ Created: Tue Jan 30 15:53:21 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaInvoker.html">CinemaInvoker</A></B></TD>
+<TD>CinemaInvoker.java
+
+
+ Created: Tue Apr 25 20:24:30 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaMenuBuilder.html">CinemaMenuBuilder</A></B></TD>
+<TD>CinemaMenuBuilder.java
+
+ This class builds a menu system based upon the module configuration
+ information.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaMultipleConsensusViewer.html">CinemaMultipleConsensusViewer</A></B></TD>
+<TD>CinemaMultipleConsensusViewer.java
+
+
+ Created: Fri Jun 23 12:09:24 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaPersist.html">CinemaPersist</A></B></TD>
+<TD>CinemaPersist.java
+
+ Provides the OptionHandler which classes need to implement persistance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaRegexp.html">CinemaRegexp</A></B></TD>
+<TD>CinemaRegexp.java
+
+ Provides support for various regexp searching facilities.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaResizeElements.html">CinemaResizeElements</A></B></TD>
+<TD>CinemaResizeElements.java
+
+
+ Created: Wed Jul 26 14:40:14 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaSlaveViewerModule.html">CinemaSlaveViewerModule</A></B></TD>
+<TD>CinemaSlaveViewerModule.java
+
+ Generates arbitrary numbers of Slave Viewers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaStatusInformation.html">CinemaStatusInformation</A></B></TD>
+<TD>CinemaStatusInformation.java
+
+ A utility class which provides what are hopefully useful status bar
+ information messages about what Cinema is currently showing.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CinemaUtilityIdentifier.html">CinemaUtilityIdentifier</A></B></TD>
+<TD>CinemaUtilityIdentifier.java
+
+
+ Created: Thu May 25 14:27:34 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A></B></TD>
+<TD>ConsensusPercentageIDColorMap.java
+
+
+ Created: Fri Jun 23 17:57:45 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/commandline/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-tree.html
new file mode 100644
index 0000000..d7b80e3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/cinema/utils/package-tree.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.cinema.utils Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.cinema.utils Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/commandline/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.cinema.utils
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html"><B>AbstractDebug</B></A> (implements uk.ac.man.bioinf.debug.<A HREF="../../../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html"><B>CinemaDebug.DebugImpl</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.html"><B>CinemaUtilityIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html"><B>CinemaFileOptionableExceptionHandler</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A>)
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>OptionableJFrame</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html"><B>CinemaAlignmentFrame</B></A> (implements java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html"><B>ConsensusPercentageIDColorMap</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, uk.ac [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html"><B>CinemaDebug</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html"><B>CinemaInvoker</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html"><B>CinemaModule</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.html"><B>CinemaGuiModule</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.html"><B>CinemaStatusInformation</B></A> (implements java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.html"><B>CinemaMenuBuilder</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.html"><B>CinemaMultipleConsensusViewer</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.htm [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.html"><B>CinemaPersist</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.html"><B>CinemaFilePersist</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.html"><B>CinemaRegexp</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.html"><B>CinemaResizeElements</B></A> (implements uk.ac.man.bioinf.apps.cinema.core.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.html">CinemaFramedActionProvider</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.cinema.utils.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.html"><B>CinemaSlaveViewerModule</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/shared/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/commandline/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html
new file mode 100644
index 0000000..be4d501
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html
@@ -0,0 +1,254 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+CalculatePercentageID
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CalculatePercentageID";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CalculatePercentageID.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.commandline</FONT>
+<BR>
+Class CalculatePercentageID</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.commandline.CalculatePercentageID</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CalculatePercentageID</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CalculatePercentageID.java
+
+
+ Created: Tue Jan 30 17:42:44 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CalculatePercentageID.java,v 1.1 2001/02/19 17:23:49 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html#CalculatePercentageID()">CalculatePercentageID</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CalculatePercentageID()"><!-- --></A><H3>
+CalculatePercentageID</H3>
+<PRE>
+public <B>CalculatePercentageID</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CalculatePercentageID.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html
new file mode 100644
index 0000000..8f5337f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+CheckMotifLocationAgainstPrints
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CheckMotifLocationAgainstPrints";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CheckMotifLocationAgainstPrints.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.commandline</FONT>
+<BR>
+Class CheckMotifLocationAgainstPrints</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.commandline.CheckMotifLocationAgainstPrints</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CheckMotifLocationAgainstPrints</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CheckMotifLocationAgainstPrints.java
+
+ This class moves through all the SequenceAlignments in the current
+ directory. It then extracts the motif information from PRINTS-S,
+ and sees whether they are still in the same position.
+
+ Created: Tue Feb 6 15:21:55 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CheckMotifLocationAgainstPrints.java,v 1.1 2001/02/19 17:23:49 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#CheckMotifLocationAgainstPrints()">CheckMotifLocationAgainstPrints</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#check(java.io.File)">check</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#checkSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.sequence.alignment.GappedSequence)">checkSequence</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> alignmentTitle,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> fprint_accn,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#openFile(java.io.File)">openFile</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> inputFile)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html#printReport()">printReport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CheckMotifLocationAgainstPrints()"><!-- --></A><H3>
+CheckMotifLocationAgainstPrints</H3>
+<PRE>
+public <B>CheckMotifLocationAgainstPrints</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printReport()"><!-- --></A><H3>
+printReport</H3>
+<PRE>
+public static void <B>printReport</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="check(java.io.File)"><!-- --></A><H3>
+check</H3>
+<PRE>
+public static void <B>check</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+checkSequence</H3>
+<PRE>
+public static void <B>checkSequence</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> alignmentTitle,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> fprint_accn,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="openFile(java.io.File)"><!-- --></A><H3>
+openFile</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>openFile</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> inputFile)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CheckMotifLocationAgainstPrints.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html
new file mode 100644
index 0000000..11f102b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+GappedSequenceSearch
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappedSequenceSearch";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/SequenceSearch.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceSearch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.commandline</FONT>
+<BR>
+Class GappedSequenceSearch</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.commandline.GappedSequenceSearch</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>GappedSequenceSearch</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceSearch.java
+
+ Searches through a SequenceAlignment specified on the command line for
+ all occurrences of the given regexp.
+
+ Created: Mon Feb 5 14:48:30 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappedSequenceSearch.java,v 1.2 2001/02/20 17:55:12 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html#GappedSequenceSearch()">GappedSequenceSearch</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GappedSequenceSearch()"><!-- --></A><H3>
+GappedSequenceSearch</H3>
+<PRE>
+public <B>GappedSequenceSearch</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/SequenceSearch.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceSearch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/SequenceSearch.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/SequenceSearch.html
new file mode 100644
index 0000000..1a6919d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/SequenceSearch.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+SequenceSearch
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceSearch";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceSearch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.commandline</FONT>
+<BR>
+Class SequenceSearch</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.commandline.SequenceSearch</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceSearch</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceSearch.java
+
+ Searches through a SequenceAlignment specified on the command line for
+ all occurrences of the given regexp.
+
+ Created: Mon Feb 5 14:48:30 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceSearch.java,v 1.2 2001/02/20 17:53:15 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/SequenceSearch.html#SequenceSearch()">SequenceSearch</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/SequenceSearch.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceSearch()"><!-- --></A><H3>
+SequenceSearch</H3>
+<PRE>
+public <B>SequenceSearch</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceSearch.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-frame.html
new file mode 100644
index 0000000..95074c0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-frame.html
@@ -0,0 +1,38 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.commandline()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.commandline()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.commandline</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="CalculatePercentageID.html" TARGET="classFrame">CalculatePercentageID</A>
+<BR>
+<A HREF="CheckMotifLocationAgainstPrints.html" TARGET="classFrame">CheckMotifLocationAgainstPrints</A>
+<BR>
+<A HREF="GappedSequenceSearch.html" TARGET="classFrame">GappedSequenceSearch</A>
+<BR>
+<A HREF="SequenceSearch.html" TARGET="classFrame">SequenceSearch</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-summary.html
new file mode 100644
index 0000000..9f55554
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-summary.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.commandline()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.commandline()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.commandline
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CalculatePercentageID.html">CalculatePercentageID</A></B></TD>
+<TD>CalculatePercentageID.java
+
+
+ Created: Tue Jan 30 17:42:44 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CheckMotifLocationAgainstPrints.html">CheckMotifLocationAgainstPrints</A></B></TD>
+<TD>CheckMotifLocationAgainstPrints.java
+
+ This class moves through all the SequenceAlignments in the current
+ directory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappedSequenceSearch.html">GappedSequenceSearch</A></B></TD>
+<TD>SequenceSearch.java
+
+ Searches through a SequenceAlignment specified on the command line for
+ all occurrences of the given regexp.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceSearch.html">SequenceSearch</A></B></TD>
+<TD>SequenceSearch.java
+
+ Searches through a SequenceAlignment specified on the command line for
+ all occurrences of the given regexp.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-tree.html
new file mode 100644
index 0000000..ecf4efb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/commandline/package-tree.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.commandline Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.commandline Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.commandline
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.commandline.<A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.html"><B>CalculatePercentageID</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.commandline.<A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.html"><B>CheckMotifLocationAgainstPrints</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.commandline.<A HREF="../../../../../../uk/ac/man/bioinf/apps/command [...]
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/AnonInvoker.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/AnonInvoker.html
new file mode 100644
index 0000000..f8958b4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/AnonInvoker.html
@@ -0,0 +1,346 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+AnonInvoker
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AnonInvoker";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AnonInvoker.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.invoker</FONT>
+<BR>
+Class AnonInvoker</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html">uk.ac.man.bioinf.apps.invoker.Invoker</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.invoker.AnonInvoker</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AnonInvoker</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A></DL>
+
+<P>
+AnonInvoker.java
+
+ This class is used with the InvokerInternalQueue. It is meant to be
+ used as a Anonymous class hence the name. The idea is that you over
+ ride the slow method with the program logic which takes a long
+ time, and is done in the Queue's thread. The doRun() method on the
+ other hand is run in the Systems main EventThread.
+
+ Parameters can be passed between the slow and fast method by the
+ "getSlowReturn" method. It is also possible to pass in a param
+ Object when OuterClass references are not appropriate.
+
+ <P>
+ Created: Mon Dec 07 13:43:59 1998
+ <P>
+ Compliant: 1.1
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AnonInvoker.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#AnonInvoker()">AnonInvoker</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#AnonInvoker(java.lang.Object)">AnonInvoker</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#AnonInvoker(java.lang.Object, java.lang.Object)">AnonInvoker</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> param)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#getSlowReturn()">getSlowReturn</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#slow()">slow</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html#slowImpl()">slowImpl</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.invoker.Invoker"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html">Invoker</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#doRun()">doRun</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#getParameter()">getParameter</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#getParameter(int)">getParameter</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#getSource()">getSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#run()">run</A [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AnonInvoker()"><!-- --></A><H3>
+AnonInvoker</H3>
+<PRE>
+public <B>AnonInvoker</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AnonInvoker(java.lang.Object)"><!-- --></A><H3>
+AnonInvoker</H3>
+<PRE>
+public <B>AnonInvoker</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AnonInvoker(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+AnonInvoker</H3>
+<PRE>
+public <B>AnonInvoker</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> param)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="slow()"><!-- --></A><H3>
+slow</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>slow</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="slowImpl()"><!-- --></A><H3>
+slowImpl</H3>
+<PRE>
+public void <B>slowImpl</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSlowReturn()"><!-- --></A><H3>
+getSlowReturn</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getSlowReturn</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AnonInvoker.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/Invoker.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/Invoker.html
new file mode 100644
index 0000000..6d03ed8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/Invoker.html
@@ -0,0 +1,439 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+Invoker
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Invoker";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Invoker.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.invoker</FONT>
+<BR>
+Class Invoker</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.invoker.Invoker</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>Invoker</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A></DL>
+
+<P>
+Invoker.java
+
+ This class another attempt at making the sytem event queue easier
+ in Swing. This class is meant to be used an a base implementation of
+ runnable with a few alternative constructors, and utility methods. Its
+ meant to be extended probably as an anonymous class to actually provide
+ any degree of functionality.
+
+ This class was originally called the "SlowInvoker". The reasons for
+ the "Slow" are entirely historical, and relatively inappropriate.
+
+ Created: Mon Dec 07 13:17:00 1998
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Invoker.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#Invoker()">Invoker</A></B>()</CODE>
+
+<BR>
+ Pointless constructor provided for the hell of it.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#Invoker(java.lang.Object)">Invoker</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source)</CODE>
+
+<BR>
+ Less Pointless constructor.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#Invoker(java.lang.Object, java.lang.Object)">Invoker</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> param)</CODE>
+
+<BR>
+ Even more less pointless contstructor
+ Takes a param to be used later as a parameter
+ for the method which will be called on what is proably
+ going to be the source.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#doRun()">doRun</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#getParameter()">getParameter</A></B>()</CODE>
+
+<BR>
+ Get the parameter</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#getParameter(int)">getParameter</A></B>(int index)</CODE>
+
+<BR>
+ Get the parameter specified by the given
+ index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#getSource()">getSource</A></B>()</CODE>
+
+<BR>
+ Get the source</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#run()">run</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html#setExceptionHandler(uk.ac.man.bioinf.util.ExceptionHandler)">setExceptionHandler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/util/ExceptionHandler.html">ExceptionHandler</A> handle)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Invoker()"><!-- --></A><H3>
+Invoker</H3>
+<PRE>
+public <B>Invoker</B>()</PRE>
+<DL>
+<DD>Pointless constructor provided for the hell of it. Might as well
+ extend Runnable directly if you use this.
+<P>
+</DL>
+<HR>
+
+<A NAME="Invoker(java.lang.Object)"><!-- --></A><H3>
+Invoker</H3>
+<PRE>
+public <B>Invoker</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source)</PRE>
+<DL>
+<DD>Less Pointless constructor.
+ Takes a parameter which is meant to be the source on the
+ anonymous class although you could clearly use it for
+ whatever you choose
+<P>
+<DT><B>Parameters:</B><DD><CODE>source</CODE> - the source or whatever you choose</DL>
+<HR>
+
+<A NAME="Invoker(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+Invoker</H3>
+<PRE>
+public <B>Invoker</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> param)</PRE>
+<DL>
+<DD>Even more less pointless contstructor
+ Takes a param to be used later as a parameter
+ for the method which will be called on what is proably
+ going to be the source. If you want to pass more than
+ one parameter then do it thru here as an array. Type checking
+ checking hell!
+<P>
+<DT><B>Parameters:</B><DD><CODE>source</CODE> - the source or whatever you chose<DD><CODE>param</CODE> - the param or whatever you choose</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="run()"><!-- --></A><H3>
+run</H3>
+<PRE>
+public void <B>run</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>run</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="doRun()"><!-- --></A><H3>
+doRun</H3>
+<PRE>
+public abstract void <B>doRun</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSource()"><!-- --></A><H3>
+getSource</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getSource</B>()</PRE>
+<DL>
+<DD>Get the source
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the source object</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParameter()"><!-- --></A><H3>
+getParameter</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getParameter</B>()</PRE>
+<DL>
+<DD>Get the parameter
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the parameter object</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getParameter(int)"><!-- --></A><H3>
+getParameter</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getParameter</B>(int index)</PRE>
+<DL>
+<DD>Get the parameter specified by the given
+ index. Note this requires a cast to
+ an array, so if this doesnt work you'll get
+ a runtime exception
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index of the parameter to be returned</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setExceptionHandler(uk.ac.man.bioinf.util.ExceptionHandler)"><!-- --></A><H3>
+setExceptionHandler</H3>
+<PRE>
+public void <B>setExceptionHandler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/util/ExceptionHandler.html">ExceptionHandler</A> handle)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Invoker.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html
new file mode 100644
index 0000000..df68d5d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html
@@ -0,0 +1,271 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+InvokerInternalEventQueueException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvokerInternalEventQueueException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerInternalEventQueueException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.invoker</FONT>
+<BR>
+Class InvokerInternalEventQueueException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>InvokerInternalEventQueueException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+InvokerInternalEventQueueException.java
+
+ For translating a generic exception into a runtime exception
+
+ Created: Fri Oct 01 15:18:01 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InvokerInternalEventQueueException.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.invoker.InvokerInternalEventQueueException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html#InvokerInternalEventQueueException(java.lang.Exception)">InvokerInternalEventQueueException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html#getException()">getException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvokerInternalEventQueueException(java.lang.Exception)"><!-- --></A><H3>
+InvokerInternalEventQueueException</H3>
+<PRE>
+public <B>InvokerInternalEventQueueException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> e)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getException()"><!-- --></A><H3>
+getException</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> <B>getException</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerInternalEventQueueException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html
new file mode 100644
index 0000000..324cbbb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html
@@ -0,0 +1,578 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+InvokerInternalQueue
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvokerInternalQueue";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerInternalQueue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.invoker</FONT>
+<BR>
+Class InvokerInternalQueue</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>InvokerInternalQueue</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></DL>
+
+<P>
+InvokerInternalQueue.java
+
+ This class is used as a helper mechanism for interacting with swing
+ objects. The idea here is that you it you can place an object on
+ this queue, and have a slow method invoked on it in a thread, and
+ then a fast method in the system event queue, without having to
+ worry about the threads themselves.
+
+ This class originally was originally called SlowInternalQueue but
+ Ive changed it because this was only due to historical reasons
+ anyway.
+
+ As this class contains an internal thread, with a reference to it,
+ it will not garbage collect by itself. It contains a "destroy()"
+ method which allows graceful shutdown. Once this method has been
+ called on an object any attempt to enqueue to the object will throw
+ an exception.
+
+ <P>
+ Created: Mon Dec 07 13:52:32 1998
+ <P>
+ Compliant:
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD></DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#systemClosing">systemClosing</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.apps.systemevents.SystemListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#NO_VETO">NO_VETO</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_ERROR">VETO_DUE_TO_ERROR</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_USER_REQUEST">VETO_DUE_TO_USER_REQUEST</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#InvokerInternalQueue()">InvokerInternalQueue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#InvokerInternalQueue(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer)">InvokerInternalQueue</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#InvokerInternalQueue(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, java.util.List)">InvokerInternalQueue</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> queue)</CODE>
+
+<BR>
+ A new queue.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ Gracefully close down the thread</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#enqueue(uk.ac.man.bioinf.apps.invoker.AnonInvoker)">enqueue</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#getOneAtATime()">getOneAtATime</A></B>()</CODE>
+
+<BR>
+ Get the value of oneAtATime.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#isDestroyed()">isDestroyed</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#makeEmpty()">makeEmpty</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#run()">run</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#setOneAtATime(boolean)">setOneAtATime</A></B>(boolean oneAtATime)</CODE>
+
+<BR>
+ Set the value of oneAtATime.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> e)</CODE>
+
+<BR>
+ This is an event listener for system events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#systemListenerPriority()">systemListenerPriority</A></B>()</CODE>
+
+<BR>
+ Some events (particularly shut downs) have to happen in a
+ very specific order.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="systemClosing"><!-- --></A><H3>
+systemClosing</H3>
+<PRE>
+public boolean <B>systemClosing</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvokerInternalQueue()"><!-- --></A><H3>
+InvokerInternalQueue</H3>
+<PRE>
+public <B>InvokerInternalQueue</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="InvokerInternalQueue(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer)"><!-- --></A><H3>
+InvokerInternalQueue</H3>
+<PRE>
+public <B>InvokerInternalQueue</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="InvokerInternalQueue(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, java.util.List)"><!-- --></A><H3>
+InvokerInternalQueue</H3>
+<PRE>
+public <B>InvokerInternalQueue</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> queue)</PRE>
+<DL>
+<DD>A new queue. This queue will listen for SystemClosing events and
+ will shut down its own thread when it hears this. The list
+ parameter needs to be a list which is mutable. This class does
+ NOT provide any synchronisation for the list, so it needs to be
+ synchronised appropriately. It practice this means it should be
+ fully synchronised!
+<P>
+<DT><B>Parameters:</B><DD><CODE>producer</CODE> - <DD><CODE>queue</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="run()"><!-- --></A><H3>
+run</H3>
+<PRE>
+public void <B>run</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>run</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="makeEmpty()"><!-- --></A><H3>
+makeEmpty</H3>
+<PRE>
+public void <B>makeEmpty</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isDestroyed()"><!-- --></A><H3>
+isDestroyed</H3>
+<PRE>
+public boolean <B>isDestroyed</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD>Gracefully close down the thread
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="enqueue(uk.ac.man.bioinf.apps.invoker.AnonInvoker)"><!-- --></A><H3>
+enqueue</H3>
+<PRE>
+public void <B>enqueue</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html">AnonInvoker</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOneAtATime()"><!-- --></A><H3>
+getOneAtATime</H3>
+<PRE>
+public boolean <B>getOneAtATime</B>()</PRE>
+<DL>
+<DD>Get the value of oneAtATime.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Value of oneAtATime.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOneAtATime(boolean)"><!-- --></A><H3>
+setOneAtATime</H3>
+<PRE>
+public void <B>setOneAtATime</B>(boolean oneAtATime)</PRE>
+<DL>
+<DD>Set the value of oneAtATime.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>oneAtATime</CODE> - Value to assign to oneAtATime.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><!-- --></A><H3>
+systemEventOccured</H3>
+<PRE>
+public void <B>systemEventOccured</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> e)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></B></DD>
+<DD>This is an event listener for system events. All listeners
+ should be signalled before the SystemEvent occurs. They should
+ not return from this method until they are ready for that event
+ to occur. An exception is thrown if the listener wishes to
+ veto this system event. g
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the system event occuring</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemListenerPriority()"><!-- --></A><H3>
+systemListenerPriority</H3>
+<PRE>
+public int <B>systemListenerPriority</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></B></DD>
+<DD>Some events (particularly shut downs) have to happen in a
+ very specific order. This method provides a priority to
+ allow this to happen. Those with the lowest priority are
+ informed first. Any valid int value is acceptable.
+ This interface does not provide the ability to set different priorities
+ for different events. The same effect can be achieved by delegating the
+ to a small class. This way a single object can register more than one
+ listener object, and thus have different priorities for different events
+ A listener should not change its priority. There is not guarentee when
+ this value will be used.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemListenerPriority()">systemListenerPriority</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerInternalQueue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html
new file mode 100644
index 0000000..907cbc9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+InvokerInternalQueueException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvokerInternalQueueException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerInternalQueueException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.invoker</FONT>
+<BR>
+Class InvokerInternalQueueException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>InvokerInternalQueueException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+InvokerInternalQueueException.java
+
+
+ Created: Fri Dec 1 17:57:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InvokerInternalQueueException.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.invoker.InvokerInternalQueueException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html#InvokerInternalQueueException(java.lang.String)">InvokerInternalQueueException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvokerInternalQueueException(java.lang.String)"><!-- --></A><H3>
+InvokerInternalQueueException</H3>
+<PRE>
+public <B>InvokerInternalQueueException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerInternalQueueException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html
new file mode 100644
index 0000000..f3acdde
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html
@@ -0,0 +1,304 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:37 BST 2002 -->
+<TITLE>
+InvokerThreadManager
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvokerThreadManager";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerThreadManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.invoker</FONT>
+<BR>
+Class InvokerThreadManager</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.invoker.InvokerThreadManager</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>InvokerThreadManager</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+InvokerThreadManager.java
+
+
+ Created: Tue Nov 7 18:47:34 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InvokerThreadManager.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#hash">hash</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#InvokerThreadManager()">InvokerThreadManager</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#getDefaultQueue()">getDefaultQueue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html#getNamedThread(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, java.lang.String)">getNamedThread</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="hash"><!-- --></A><H3>
+hash</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/HashMap.html">HashMap</A> <B>hash</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvokerThreadManager()"><!-- --></A><H3>
+InvokerThreadManager</H3>
+<PRE>
+public <B>InvokerThreadManager</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getDefaultQueue()"><!-- --></A><H3>
+getDefaultQueue</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> <B>getDefaultQueue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNamedThread(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, java.lang.String)"><!-- --></A><H3>
+getNamedThread</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> <B>getNamedThread</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvokerThreadManager.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-frame.html
new file mode 100644
index 0000000..42490ec
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-frame.html
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.invoker()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.invoker()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.invoker</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AnonInvoker.html" TARGET="classFrame">AnonInvoker</A>
+<BR>
+<A HREF="Invoker.html" TARGET="classFrame">Invoker</A>
+<BR>
+<A HREF="InvokerInternalQueue.html" TARGET="classFrame">InvokerInternalQueue</A>
+<BR>
+<A HREF="InvokerThreadManager.html" TARGET="classFrame">InvokerThreadManager</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="InvokerInternalEventQueueException.html" TARGET="classFrame">InvokerInternalEventQueueException</A>
+<BR>
+<A HREF="InvokerInternalQueueException.html" TARGET="classFrame">InvokerInternalQueueException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-summary.html
new file mode 100644
index 0000000..527ac8a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-summary.html
@@ -0,0 +1,182 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.invoker()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.invoker()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.invoker
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AnonInvoker.html">AnonInvoker</A></B></TD>
+<TD>AnonInvoker.java
+
+ This class is used with the InvokerInternalQueue.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Invoker.html">Invoker</A></B></TD>
+<TD>Invoker.java
+
+ This class another attempt at making the sytem event queue easier
+ in Swing.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvokerInternalQueue.html">InvokerInternalQueue</A></B></TD>
+<TD>InvokerInternalQueue.java
+
+ This class is used as a helper mechanism for interacting with swing
+ objects.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvokerThreadManager.html">InvokerThreadManager</A></B></TD>
+<TD>InvokerThreadManager.java
+
+
+ Created: Tue Nov 7 18:47:34 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvokerInternalEventQueueException.html">InvokerInternalEventQueueException</A></B></TD>
+<TD>InvokerInternalEventQueueException.java
+
+ For translating a generic exception into a runtime exception
+
+ Created: Fri Oct 01 15:18:01 1999</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvokerInternalQueueException.html">InvokerInternalQueueException</A></B></TD>
+<TD>InvokerInternalQueueException.java
+
+
+ Created: Fri Dec 1 17:57:48 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-tree.html
new file mode 100644
index 0000000..b6686ad
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/invoker/package-tree.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.invoker Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.invoker Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.invoker
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/Invoker.html"><B>Invoker</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/AnonInvoker.html"><B>AnonInvoker</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html"><B>InvokerInternalQueue</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Runnable.html">Runnable</A>, uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.html"><B>InvokerThreadManager</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.html"><B>InvokerInternalEventQueueException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.invoker.<A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.html"><B>InvokerInternalQueueException</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/commandline/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html
new file mode 100644
index 0000000..48bda52
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html
@@ -0,0 +1,321 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+FileSaveableOptions
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FileSaveableOptions";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSaveableOptions.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Class FileSaveableOptions</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">uk.ac.man.bioinf.apps.optionable.SaveableOptions</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.optionable.FileSaveableOptions</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileSaveableOptions</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A></DL>
+
+<P>
+FileSaveableOptions.java
+
+ Provides Saveable Option support with files.
+
+ Created: Tue Feb 02 16:40:27 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FileSaveableOptions.java,v 1.16 2001/05/14 17:08:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.apps.systemevents.SystemListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#NO_VETO">NO_VETO</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_ERROR">VETO_DUE_TO_ERROR</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_USER_REQUEST">VETO_DUE_TO_USER_REQUEST</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html#FileSaveableOptions(java.io.File, uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)">FileSaveableOptions</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> configFile,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A> exHandler)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html#getLoadStream()">getLoadStream</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/OutputStream.html">OutputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html#getSaveStream()">getSaveStream</A></B>()</CODE>
+
+<BR>
+ These were originally going to be abstract but you cant make
+ abstract static methods.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.apps.optionable.SaveableOptions"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">addOptionable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getExceptionHandler()">getExceptionHandler</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#loadOptions()">loadOptions</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileSaveableOptions(java.io.File, uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)"><!-- --></A><H3>
+FileSaveableOptions</H3>
+<PRE>
+public <B>FileSaveableOptions</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> configFile,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A> exHandler)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSaveStream()"><!-- --></A><H3>
+getSaveStream</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/OutputStream.html">OutputStream</A> <B>getSaveStream</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD>These were originally going to be abstract but you cant make
+ abstract static methods. I guess its no big thing as thing is
+ pretty much a one off class anyway.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getSaveStream()">getSaveStream</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLoadStream()"><!-- --></A><H3>
+getLoadStream</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>getLoadStream</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getLoadStream()">getLoadStream</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSaveableOptions.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html
new file mode 100644
index 0000000..1c6eca8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html
@@ -0,0 +1,315 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+NullOptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NullOptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullOptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Class NullOptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.optionable.NullOptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NullOptionHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></DL>
+
+<P>
+NullOptionHandler.java
+
+ An option handler object that does nothing.
+
+ Created: Thu Feb 1 17:42:05 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NullOptionHandler.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">addOptionable</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Add an optionable object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">removeOptionable</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Remove the following optionable object from
+ the list</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)">requestOptionUpdate</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Request that the optionable object set the the options
+ of the optionable object via its setOptions method.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+addOptionable</H3>
+<PRE>
+public void <B>addOptionable</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></B></DD>
+<DD>Add an optionable object. On adding the Optionhandler
+ should set itself as the OptionHandler for the optionable
+ object, and call requestOptionUpdate also.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">addOptionable</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+removeOptionable</H3>
+<PRE>
+public void <B>removeOptionable</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></B></DD>
+<DD>Remove the following optionable object from
+ the list
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">removeOptionable</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionable</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+requestOptionUpdate</H3>
+<PRE>
+public void <B>requestOptionUpdate</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></B></DD>
+<DD>Request that the optionable object set the the options
+ of the optionable object via its setOptions method. This could
+ be used for a variety of reasons, although the most obvious
+ is a "revert to saved" option.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)">requestOptionUpdate</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionable</CODE> - the optionable object<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)"><CODE>Optionable.setOptions(java.lang.Object)</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullOptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionHandler.html
new file mode 100644
index 0000000..ba45f0d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionHandler.html
@@ -0,0 +1,269 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+OptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="OptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Interface OptionHandler</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html">NullOptionHandler</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>OptionHandler</B></DL>
+
+<P>
+OptionHandler.java
+
+ Objects implementing this interface should record all of
+ Optionable object, storing and restoring their options
+ as necessary
+
+ Created: Mon Feb 01 18:10:52 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: OptionHandler.java,v 1.7 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">addOptionable</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Add an optionable object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">removeOptionable</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Remove the following optionable object from
+ the list</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)">requestOptionUpdate</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Request that the optionable object set the the options
+ of the optionable object via its setOptions method.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+addOptionable</H3>
+<PRE>
+public void <B>addOptionable</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD>Add an optionable object. On adding the Optionhandler
+ should set itself as the OptionHandler for the optionable
+ object, and call requestOptionUpdate also.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+removeOptionable</H3>
+<PRE>
+public void <B>removeOptionable</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD>Remove the following optionable object from
+ the list
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionable</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+requestOptionUpdate</H3>
+<PRE>
+public void <B>requestOptionUpdate</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD>Request that the optionable object set the the options
+ of the optionable object via its setOptions method. This could
+ be used for a variety of reasons, although the most obvious
+ is a "revert to saved" option.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionable</CODE> - the optionable object<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)"><CODE>Optionable.setOptions(java.lang.Object)</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/Optionable.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/Optionable.html
new file mode 100644
index 0000000..8db2b4c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/Optionable.html
@@ -0,0 +1,324 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+Optionable
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Optionable";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Optionable.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Interface Optionable</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html">OptionableJFrame</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html">OptionableJSplitPane</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Optionable</B></DL>
+
+<P>
+Optionable.java
+
+ An object implementing this interface may be in several
+ different states, that is provide options. These options
+ can then be stored or in other ways treated at some
+ time point, and may also need to be set at some point. Essentially
+ this interface was written to provide an easy way of serialising
+ user defined options.
+
+ The options should be provided in the form of a hashtable.
+ Every Optionable object must provide a name by which it wants
+ to group its options, so that instances of an object do not
+ (necessarily) conflict with each others options
+ Created: Mon Feb 01 16:11:12 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Optionable.java,v 1.6 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionGroupName()">getOptionGroupName</A></B>()</CODE>
+
+<BR>
+ This string is used as an identifier for the groups
+ of options.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionHandler()">getOptionHandler</A></B>()</CODE>
+
+<BR>
+ Get the value of OptionHandler.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptions()">getOptions</A></B>()</CODE>
+
+<BR>
+ This method provides the current state of object as a map
+ of objects</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setOptionHandler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> OptionHandler)</CODE>
+
+<BR>
+ Set the value of OptionHandler.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)">setOptions</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> options)</CODE>
+
+<BR>
+ Sets the options for this object</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getOptionGroupName()"><!-- --></A><H3>
+getOptionGroupName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getOptionGroupName</B>()</PRE>
+<DL>
+<DD>This string is used as an identifier for the groups
+ of options. It will probably be used on a per-instance
+ basis, but could also be shared by all members of a class
+ or by an entire application. It should probably however
+ remain constant over time for any given Optionable object
+ If more than one optionable object is registered with
+ the same option handler and have the same group name the
+ options retrieved from one object will over ride all of the
+ others.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the string by the group of options is known</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptions()"><!-- --></A><H3>
+getOptions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getOptions</B>()</PRE>
+<DL>
+<DD>This method provides the current state of object as a map
+ of objects
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the options</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptions(java.lang.Object)"><!-- --></A><H3>
+setOptions</H3>
+<PRE>
+public void <B>setOptions</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> options)</PRE>
+<DL>
+<DD>Sets the options for this object
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionHandler()"><!-- --></A><H3>
+getOptionHandler</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getOptionHandler</B>()</PRE>
+<DL>
+<DD>Get the value of OptionHandler.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Value of OptionHandler.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><!-- --></A><H3>
+setOptionHandler</H3>
+<PRE>
+public void <B>setOptionHandler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> OptionHandler)</PRE>
+<DL>
+<DD>Set the value of OptionHandler.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>OptionHandler</CODE> - the value to assign to OptionHandler</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Optionable.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html
new file mode 100644
index 0000000..4146418
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html
@@ -0,0 +1,333 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+OptionableExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="OptionableExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Interface OptionableExceptionHandler</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.html">CinemaFileOptionableExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>OptionableExceptionHandler</B></DL>
+
+<P>
+OptionableExceptionHandler.java
+
+
+ Created: Mon May 14 14:04:22 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: OptionableExceptionHandler.java,v 1.1 2001/05/14 17:08:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.lang.ClassNotFoundException)">handleLoadException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ClassNotFoundException.html">ClassNotFoundException</A> exp)</CODE>
+
+<BR>
+ ClassNotFoundException can occur when reading data from the
+ stream for a data type that does not exist.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.lang.Exception)">handleLoadException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</CODE>
+
+<BR>
+ Handle an exception occurring during the loading of options.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(java.io.IOException)">handleLoadException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> iop)</CODE>
+
+<BR>
+ Signalled if some unknown IOException occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)">handleLoadException</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A> osnfe)</CODE>
+
+<BR>
+ If the optionable load file can not be found this error is signalled.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleSaveException(java.lang.Exception)">handleSaveException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</CODE>
+
+<BR>
+ If something nasty occurs whilst gather the optionable
+ information occurs this is error is signalled.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html#handleSaveException(java.io.IOException)">handleSaveException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> io)</CODE>
+
+<BR>
+ If the save encounters IO problems!</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleLoadException(java.lang.Exception)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</PRE>
+<DL>
+<DD>Handle an exception occurring during the loading of options.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> -
+<DT><B>Returns:</B><DD>true if the an attempt should be made to load the options
+ again.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleLoadException(java.lang.ClassNotFoundException)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ClassNotFoundException.html">ClassNotFoundException</A> exp)</PRE>
+<DL>
+<DD>ClassNotFoundException can occur when reading data from the
+ stream for a data type that does not exist. It won't normally
+ occur.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleLoadException(java.io.IOException)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> iop)</PRE>
+<DL>
+<DD>Signalled if some unknown IOException occurs
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>iop</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleLoadException(uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException)"><!-- --></A><H3>
+handleLoadException</H3>
+<PRE>
+public boolean <B>handleLoadException</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A> osnfe)</PRE>
+<DL>
+<DD>If the optionable load file can not be found this error is signalled.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>osnfe</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleSaveException(java.lang.Exception)"><!-- --></A><H3>
+handleSaveException</H3>
+<PRE>
+public boolean <B>handleSaveException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A> exp)</PRE>
+<DL>
+<DD>If something nasty occurs whilst gather the optionable
+ information occurs this is error is signalled.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="handleSaveException(java.io.IOException)"><!-- --></A><H3>
+handleSaveException</H3>
+<PRE>
+public boolean <B>handleSaveException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A> io)</PRE>
+<DL>
+<DD>If the save encounters IO problems!
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>io</CODE> -
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html
new file mode 100644
index 0000000..2d9ab12
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+OptionableSourceNotFoundException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="OptionableSourceNotFoundException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableSourceNotFoundException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Class OptionableSourceNotFoundException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">java.io.IOException</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>OptionableSourceNotFoundException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></DL>
+
+<P>
+OptionableSourceNotFoundException.java
+
+
+ Created: Mon May 14 14:13:40 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: OptionableSourceNotFoundException.java,v 1.1 2001/05/14 17:08:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html#OptionableSourceNotFoundException()">OptionableSourceNotFoundException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html#OptionableSourceNotFoundException(java.lang.String)">OptionableSourceNotFoundException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="OptionableSourceNotFoundException()"><!-- --></A><H3>
+OptionableSourceNotFoundException</H3>
+<PRE>
+public <B>OptionableSourceNotFoundException</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="OptionableSourceNotFoundException(java.lang.String)"><!-- --></A><H3>
+OptionableSourceNotFoundException</H3>
+<PRE>
+public <B>OptionableSourceNotFoundException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableSourceNotFoundException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableStateException.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableStateException.html
new file mode 100644
index 0000000..e07e433
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/OptionableStateException.html
@@ -0,0 +1,239 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+OptionableStateException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="OptionableStateException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableStateException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Class OptionableStateException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.optionable.OptionableStateException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>OptionableStateException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A></DL>
+
+<P>
+OptionableStateException.java
+
+ This exception is thrown when an Optionable object is in an illegal
+ state. This normally indicates that an attempt to set the
+ Optionable state of an object that has already been set.
+
+ Created: Thu Feb 1 20:39:43 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: OptionableStateException.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.optionable.OptionableStateException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html#OptionableStateException(java.lang.String)">OptionableStateException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="OptionableStateException(java.lang.String)"><!-- --></A><H3>
+OptionableStateException</H3>
+<PRE>
+public <B>OptionableStateException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableStateException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/SaveableOptions.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/SaveableOptions.html
new file mode 100644
index 0000000..2b1ee1a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/SaveableOptions.html
@@ -0,0 +1,497 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:38 BST 2002 -->
+<TITLE>
+SaveableOptions
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SaveableOptions";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SaveableOptions.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.optionable</FONT>
+<BR>
+Class SaveableOptions</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.optionable.SaveableOptions</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html">FileSaveableOptions</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>SaveableOptions</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></DL>
+
+<P>
+SaveableOptions.java
+
+ This class is used to initilise and save all of the necessary
+ options required. This class is fully synchronized
+ Created: Tue Feb 02 16:40:27 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SaveableOptions.java,v 1.16 2001/05/14 17:08:18 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.apps.systemevents.SystemListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#NO_VETO">NO_VETO</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_ERROR">VETO_DUE_TO_ERROR</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_USER_REQUEST">VETO_DUE_TO_USER_REQUEST</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#SaveableOptions(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)">SaveableOptions</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A> exHandler)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">addOptionable</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Add an optionable object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getExceptionHandler()">getExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getLoadStream()">getLoadStream</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/OutputStream.html">OutputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#getSaveStream()">getSaveStream</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#loadOptions()">loadOptions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">removeOptionable</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Remove the following optionable object from
+ the list</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)">requestOptionUpdate</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</CODE>
+
+<BR>
+ Request that the optionable object set the the options
+ of the optionable object via its setOptions method.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> event)</CODE>
+
+<BR>
+ This is an event listener for system events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html#systemListenerPriority()">systemListenerPriority</A></B>()</CODE>
+
+<BR>
+ Some events (particularly shut downs) have to happen in a
+ very specific order.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SaveableOptions(uk.ac.man.bioinf.apps.systemevents.SystemEventProducer, uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler)"><!-- --></A><H3>
+SaveableOptions</H3>
+<PRE>
+public <B>SaveableOptions</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A> producer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A> exHandler)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getExceptionHandler()"><!-- --></A><H3>
+getExceptionHandler</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html">OptionableExceptionHandler</A> <B>getExceptionHandler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><!-- --></A><H3>
+systemEventOccured</H3>
+<PRE>
+public void <B>systemEventOccured</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></B></DD>
+<DD>This is an event listener for system events. All listeners
+ should be signalled before the SystemEvent occurs. They should
+ not return from this method until they are ready for that event
+ to occur. An exception is thrown if the listener wishes to
+ veto this system event. g
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the system event occuring</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemListenerPriority()"><!-- --></A><H3>
+systemListenerPriority</H3>
+<PRE>
+public int <B>systemListenerPriority</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></B></DD>
+<DD>Some events (particularly shut downs) have to happen in a
+ very specific order. This method provides a priority to
+ allow this to happen. Those with the lowest priority are
+ informed first. Any valid int value is acceptable.
+ This interface does not provide the ability to set different priorities
+ for different events. The same effect can be achieved by delegating the
+ to a small class. This way a single object can register more than one
+ listener object, and thus have different priorities for different events
+ A listener should not change its priority. There is not guarentee when
+ this value will be used.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemListenerPriority()">systemListenerPriority</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSaveStream()"><!-- --></A><H3>
+getSaveStream</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/OutputStream.html">OutputStream</A> <B>getSaveStream</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLoadStream()"><!-- --></A><H3>
+getLoadStream</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>getLoadStream</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="loadOptions()"><!-- --></A><H3>
+loadOptions</H3>
+<PRE>
+protected void <B>loadOptions</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+addOptionable</H3>
+<PRE>
+public void <B>addOptionable</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></B></DD>
+<DD>Add an optionable object. On adding the Optionhandler
+ should set itself as the OptionHandler for the optionable
+ object, and call requestOptionUpdate also.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#addOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">addOptionable</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+removeOptionable</H3>
+<PRE>
+public void <B>removeOptionable</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></B></DD>
+<DD>Remove the following optionable object from
+ the list
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#removeOptionable(uk.ac.man.bioinf.apps.optionable.Optionable)">removeOptionable</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionable</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)"><!-- --></A><H3>
+requestOptionUpdate</H3>
+<PRE>
+public void <B>requestOptionUpdate</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A> optionable)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></B></DD>
+<DD>Request that the optionable object set the the options
+ of the optionable object via its setOptions method. This could
+ be used for a variety of reasons, although the most obvious
+ is a "revert to saved" option.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html#requestOptionUpdate(uk.ac.man.bioinf.apps.optionable.Optionable)">requestOptionUpdate</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionable</CODE> - the optionable object<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)"><CODE>Optionable.setOptions(java.lang.Object)</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SaveableOptions.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-frame.html
new file mode 100644
index 0000000..7cd1926
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-frame.html
@@ -0,0 +1,64 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.optionable()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.optionable()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.optionable</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Optionable.html" TARGET="classFrame"><I>Optionable</I></A>
+<BR>
+<A HREF="OptionableExceptionHandler.html" TARGET="classFrame"><I>OptionableExceptionHandler</I></A>
+<BR>
+<A HREF="OptionHandler.html" TARGET="classFrame"><I>OptionHandler</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="FileSaveableOptions.html" TARGET="classFrame">FileSaveableOptions</A>
+<BR>
+<A HREF="NullOptionHandler.html" TARGET="classFrame">NullOptionHandler</A>
+<BR>
+<A HREF="SaveableOptions.html" TARGET="classFrame">SaveableOptions</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="OptionableSourceNotFoundException.html" TARGET="classFrame">OptionableSourceNotFoundException</A>
+<BR>
+<A HREF="OptionableStateException.html" TARGET="classFrame">OptionableStateException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-summary.html
new file mode 100644
index 0000000..bffc2be
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-summary.html
@@ -0,0 +1,207 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.optionable()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.optionable()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.optionable
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Optionable.html"><I>Optionable</I></A></B></TD>
+<TD>Optionable.java
+
+ An object implementing this interface may be in several
+ different states, that is provide options.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="OptionableExceptionHandler.html"><I>OptionableExceptionHandler</I></A></B></TD>
+<TD>OptionableExceptionHandler.java
+
+
+ Created: Mon May 14 14:04:22 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="OptionHandler.html"><I>OptionHandler</I></A></B></TD>
+<TD>OptionHandler.java
+
+ Objects implementing this interface should record all of
+ Optionable object, storing and restoring their options
+ as necessary
+
+ Created: Mon Feb 01 18:10:52 1999</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FileSaveableOptions.html">FileSaveableOptions</A></B></TD>
+<TD>FileSaveableOptions.java
+
+ Provides Saveable Option support with files.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NullOptionHandler.html">NullOptionHandler</A></B></TD>
+<TD>NullOptionHandler.java
+
+ An option handler object that does nothing.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SaveableOptions.html">SaveableOptions</A></B></TD>
+<TD>SaveableOptions.java
+
+ This class is used to initilise and save all of the necessary
+ options required.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="OptionableSourceNotFoundException.html">OptionableSourceNotFoundException</A></B></TD>
+<TD>OptionableSourceNotFoundException.java
+
+
+ Created: Mon May 14 14:13:40 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="OptionableStateException.html">OptionableStateException</A></B></TD>
+<TD>OptionableStateException.java
+
+ This exception is thrown when an Optionable object is in an illegal
+ state.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-tree.html
new file mode 100644
index 0000000..17422ad
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/optionable/package-tree.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.optionable Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.optionable Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.optionable
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/NullOptionHandler.html"><B>NullOptionHandler</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html"><B>SaveableOptions</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A>, uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.html"><B>FileSaveableOptions</B></A></UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html"><B>IOException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.html"><B>OptionableSourceNotFoundException</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html"><B>OptionableStateException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html"><B>Optionable</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.html"><B>OptionableExceptionHandler</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">< [...]
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEvent.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEvent.html
new file mode 100644
index 0000000..323203e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEvent.html
@@ -0,0 +1,287 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+SystemEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SystemEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.systemevents</FONT>
+<BR>
+Class SystemEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.systemevents.SystemEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SystemEvent</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></DL>
+
+<P>
+SystemEvent.java
+
+
+ <P>
+ Created: Thu Jan 14 17:51:04 1999
+ <P>
+ Compliant:
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD></DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.systemevents.SystemEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html#SystemEvent(java.lang.Object, uk.ac.man.bioinf.apps.systemevents.SystemEventOption)">SystemEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> option)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html#getOption()">getOption</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SystemEvent(java.lang.Object, uk.ac.man.bioinf.apps.systemevents.SystemEventOption)"><!-- --></A><H3>
+SystemEvent</H3>
+<PRE>
+public <B>SystemEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> option)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getOption()"><!-- --></A><H3>
+getOption</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> <B>getOption</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html
new file mode 100644
index 0000000..45c70f5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html
@@ -0,0 +1,262 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+SystemEventOption
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SystemEventOption";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEventOption.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.systemevents</FONT>
+<BR>
+Class SystemEventOption</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.systemevents.SystemEventOption</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SystemEventOption</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SystemEventOption.java
+
+
+ <P>
+ Created: Thu Jan 14 17:54:34 1999
+ <P>
+ Compliant:
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD></DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html#SYSTEM_SHUTDOWN">SYSTEM_SHUTDOWN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SYSTEM_SHUTDOWN"><!-- --></A><H3>
+SYSTEM_SHUTDOWN</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> <B>SYSTEM_SHUTDOWN</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEventOption.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html
new file mode 100644
index 0000000..8a8c609
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+SystemEventProducer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SystemEventProducer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEventProducer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.systemevents</FONT>
+<BR>
+Interface SystemEventProducer</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.html">CinemaSystemEvents</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html">SystemEventSupport</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SystemEventProducer</B></DL>
+
+<P>
+SystemEventProducer.java
+
+ Interface defining the SystemEventProducer
+
+ Created: Fri Oct 01 14:55:42 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SystemEventProducer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">addSystemEventListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">removeSystemEventListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><!-- --></A><H3>
+addSystemEventListener</H3>
+<PRE>
+public void <B>addSystemEventListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><!-- --></A><H3>
+removeSystemEventListener</H3>
+<PRE>
+public void <B>removeSystemEventListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEventProducer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html
new file mode 100644
index 0000000..2f7cf76
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html
@@ -0,0 +1,334 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+SystemEventSupport
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SystemEventSupport";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEventSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.systemevents</FONT>
+<BR>
+Class SystemEventSupport</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.systemevents.SystemEventSupport</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SystemEventSupport</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></DL>
+
+<P>
+SystemEventSupport.java
+
+ Provides a basic queue for holding all the listeners. Im using
+ a priority queue here.
+
+ Created: Thu Apr 15 17:44:57 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SystemEventSupport.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#SystemEventSupport()">SystemEventSupport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">addSystemEventListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#fireSystemEvent(uk.ac.man.bioinf.apps.systemevents.SystemEventOption)">fireSystemEvent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> option)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#getLastPriorityRun()">getLastPriorityRun</A></B>()</CODE>
+
+<BR>
+ The priority of the last listener which this class attempted to
+ inform of a system event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">removeSystemEventListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SystemEventSupport()"><!-- --></A><H3>
+SystemEventSupport</H3>
+<PRE>
+public <B>SystemEventSupport</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><!-- --></A><H3>
+addSystemEventListener</H3>
+<PRE>
+public void <B>addSystemEventListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#addSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">addSystemEventListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)"><!-- --></A><H3>
+removeSystemEventListener</H3>
+<PRE>
+public void <B>removeSystemEventListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html">SystemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html#removeSystemEventListener(uk.ac.man.bioinf.apps.systemevents.SystemListener)">removeSystemEventListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEventProducer</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireSystemEvent(uk.ac.man.bioinf.apps.systemevents.SystemEventOption)"><!-- --></A><H3>
+fireSystemEvent</H3>
+<PRE>
+public void <B>fireSystemEvent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html">SystemEventOption</A> option)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLastPriorityRun()"><!-- --></A><H3>
+getLastPriorityRun</H3>
+<PRE>
+public int <B>getLastPriorityRun</B>()</PRE>
+<DL>
+<DD>The priority of the last listener which this class attempted to
+ inform of a system event. If the runSystemEvent throws an exception
+ this method will therefore be the priority of the listener throwing
+ that exception
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemEventSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemListener.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemListener.html
new file mode 100644
index 0000000..15c203c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemListener.html
@@ -0,0 +1,348 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+SystemListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SystemListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.systemevents</FONT>
+<BR>
+Interface SystemListener</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/SaveableOptions.html">SaveableOptions</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SystemListener</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DL>
+
+<P>
+SystemListener.java
+
+ Listeners to system events. At the moment this consists of ShutDown events
+
+ <P>
+ Created: Thu Jan 14 17:48:54 1999
+ <P>
+ Compliant:
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD></DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#NO_VETO">NO_VETO</A></B></CODE>
+
+<BR>
+ This value should be used when the system is going to
+ shutdown regardless of errors</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_ERROR">VETO_DUE_TO_ERROR</A></B></CODE>
+
+<BR>
+ This value should be used when the System shutdown can
+ not be aborted unless there is some error in the shutdown
+ procedure</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#VETO_DUE_TO_USER_REQUEST">VETO_DUE_TO_USER_REQUEST</A></B></CODE>
+
+<BR>
+ This value should be used when the user has full control
+ over aborting the shutdown.</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)">systemEventOccured</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> e)</CODE>
+
+<BR>
+ This is an event listener for system events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html#systemListenerPriority()">systemListenerPriority</A></B>()</CODE>
+
+<BR>
+ Some events (particularly shut downs) have to happen in a
+ very specific order.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="VETO_DUE_TO_ERROR"><!-- --></A><H3>
+VETO_DUE_TO_ERROR</H3>
+<PRE>
+public static final int <B>VETO_DUE_TO_ERROR</B></PRE>
+<DL>
+<DD>This value should be used when the System shutdown can
+ not be aborted unless there is some error in the shutdown
+ procedure
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.apps.systemevents.SystemListener.VETO_DUE_TO_ERROR">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="VETO_DUE_TO_USER_REQUEST"><!-- --></A><H3>
+VETO_DUE_TO_USER_REQUEST</H3>
+<PRE>
+public static final int <B>VETO_DUE_TO_USER_REQUEST</B></PRE>
+<DL>
+<DD>This value should be used when the user has full control
+ over aborting the shutdown.
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.apps.systemevents.SystemListener.VETO_DUE_TO_USER_REQUEST">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="NO_VETO"><!-- --></A><H3>
+NO_VETO</H3>
+<PRE>
+public static final int <B>NO_VETO</B></PRE>
+<DL>
+<DD>This value should be used when the system is going to
+ shutdown regardless of errors
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.apps.systemevents.SystemListener.NO_VETO">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="systemEventOccured(uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><!-- --></A><H3>
+systemEventOccured</H3>
+<PRE>
+public void <B>systemEventOccured</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> e)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></PRE>
+<DL>
+<DD>This is an event listener for system events. All listeners
+ should be signalled before the SystemEvent occurs. They should
+ not return from this method until they are ready for that event
+ to occur. An exception is thrown if the listener wishes to
+ veto this system event. g
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the system event occuring
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html">SystemVetoException</A></CODE> - if the listener does not want the event to happen</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="systemListenerPriority()"><!-- --></A><H3>
+systemListenerPriority</H3>
+<PRE>
+public int <B>systemListenerPriority</B>()</PRE>
+<DL>
+<DD>Some events (particularly shut downs) have to happen in a
+ very specific order. This method provides a priority to
+ allow this to happen. Those with the lowest priority are
+ informed first. Any valid int value is acceptable.
+ This interface does not provide the ability to set different priorities
+ for different events. The same effect can be achieved by delegating the
+ to a small class. This way a single object can register more than one
+ listener object, and thus have different priorities for different events
+ A listener should not change its priority. There is not guarentee when
+ this value will be used.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html
new file mode 100644
index 0000000..76d1dc8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+SystemVetoException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SystemVetoException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemVetoException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.systemevents</FONT>
+<BR>
+Class SystemVetoException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.systemevents.SystemVetoException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SystemVetoException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A></DL>
+
+<P>
+SystemVetoException.java
+
+
+ Created: Thu Apr 15 17:23:20 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SystemVetoException.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.apps.systemevents.SystemVetoException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html#SystemVetoException(java.lang.String, uk.ac.man.bioinf.apps.systemevents.SystemEvent)">SystemVetoException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html#getSystemEvent()">getSystemEvent</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SystemVetoException(java.lang.String, uk.ac.man.bioinf.apps.systemevents.SystemEvent)"><!-- --></A><H3>
+SystemVetoException</H3>
+<PRE>
+public <B>SystemVetoException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> event)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSystemEvent()"><!-- --></A><H3>
+getSystemEvent</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html">SystemEvent</A> <B>getSystemEvent</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SystemVetoException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-frame.html
new file mode 100644
index 0000000..e6d625d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-frame.html
@@ -0,0 +1,60 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.systemevents()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.systemevents()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.systemevents</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SystemEventProducer.html" TARGET="classFrame"><I>SystemEventProducer</I></A>
+<BR>
+<A HREF="SystemListener.html" TARGET="classFrame"><I>SystemListener</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SystemEvent.html" TARGET="classFrame">SystemEvent</A>
+<BR>
+<A HREF="SystemEventOption.html" TARGET="classFrame">SystemEventOption</A>
+<BR>
+<A HREF="SystemEventSupport.html" TARGET="classFrame">SystemEventSupport</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SystemVetoException.html" TARGET="classFrame">SystemVetoException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-summary.html
new file mode 100644
index 0000000..fd4941a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-summary.html
@@ -0,0 +1,191 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.systemevents()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.systemevents()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.systemevents
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SystemEventProducer.html"><I>SystemEventProducer</I></A></B></TD>
+<TD>SystemEventProducer.java
+
+ Interface defining the SystemEventProducer
+
+ Created: Fri Oct 01 14:55:42 1999</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SystemListener.html"><I>SystemListener</I></A></B></TD>
+<TD>SystemListener.java
+
+ Listeners to system events.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SystemEvent.html">SystemEvent</A></B></TD>
+<TD>SystemEvent.java
+
+
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SystemEventOption.html">SystemEventOption</A></B></TD>
+<TD>SystemEventOption.java
+
+
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SystemEventSupport.html">SystemEventSupport</A></B></TD>
+<TD>SystemEventSupport.java
+
+ Provides a basic queue for holding all the listeners.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SystemVetoException.html">SystemVetoException</A></B></TD>
+<TD>SystemVetoException.java
+
+
+ Created: Thu Apr 15 17:23:20 1999</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-tree.html
new file mode 100644
index 0000000..7009613
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/systemevents/package-tree.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.systemevents Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.systemevents Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.systemevents
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html"><B>EventObject</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEvent.html"><B>SystemEvent</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventOption.html"><B>SystemEventOption</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.html"><B>SystemEventSupport</B></A> (implements uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html">SystemEv [...]
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemVetoException.html"><B>SystemVetoException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html"><B>EventListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemListener.html"><B>SystemListener</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.systemevents.<A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.html"><B>SystemEventProducer</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/ConfigNode.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/ConfigNode.html
new file mode 100644
index 0000000..2ccf809
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/ConfigNode.html
@@ -0,0 +1,373 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+ConfigNode
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ConfigNode";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConfigNode.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class ConfigNode</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.ConfigNode</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ConfigNode</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ConfigNode.java
+
+
+ Created: Tue May 9 21:45:13 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ConfigNode.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#ConfigNode()">ConfigNode</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#addChildNode(uk.ac.man.bioinf.apps.xml.ConfigNode)">addChildNode</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> node)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#getChildNodes()">getChildNodes</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#getModuleData()">getModuleData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#getStringData()">getStringData</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#isModuleIdentifier()">isModuleIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#setData(uk.ac.man.bioinf.module.ModuleIdentifier)">setData</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> moduleIdentifer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html#setData(java.lang.String)">setData</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> data)</CODE>
+
+<BR>
+ Set the data for this config node.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ConfigNode()"><!-- --></A><H3>
+ConfigNode</H3>
+<PRE>
+public <B>ConfigNode</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addChildNode(uk.ac.man.bioinf.apps.xml.ConfigNode)"><!-- --></A><H3>
+addChildNode</H3>
+<PRE>
+public void <B>addChildNode</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> node)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getChildNodes()"><!-- --></A><H3>
+getChildNodes</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A>[] <B>getChildNodes</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setData(java.lang.String)"><!-- --></A><H3>
+setData</H3>
+<PRE>
+public void <B>setData</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> data)</PRE>
+<DL>
+<DD>Set the data for this config node.
+ This data is of the form ("MOD:"|"VAL:")data where data is the
+ data which will be returned, and the first bit shows whether this
+ is a module or not.
+ (PENDING:- PL) This is really crap, and I think that there is no
+ necessity for all this daft string matching. Need to remove it.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>data</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setData(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+setData</H3>
+<PRE>
+public void <B>setData</B>(<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> moduleIdentifer)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModuleIdentifier()"><!-- --></A><H3>
+isModuleIdentifier</H3>
+<PRE>
+public boolean <B>isModuleIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getStringData()"><!-- --></A><H3>
+getStringData</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getStringData</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModuleData()"><!-- --></A><H3>
+getModuleData</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>getModuleData</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ConfigNode.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html
new file mode 100644
index 0000000..24f7508
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html
@@ -0,0 +1,258 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+DefaultXMLParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultXMLParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultXMLParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class DefaultXMLParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.DefaultXMLParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultXMLParser</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A></DL>
+
+<P>
+DefaultXMLParser.java
+
+
+ Created: Mon May 8 21:08:32 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultXMLParser.java,v 1.5 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html#DefaultXMLParser()">DefaultXMLParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> org.xml.sax.XMLReader</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html#getXMLParser()">getXMLParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultXMLParser()"><!-- --></A><H3>
+DefaultXMLParser</H3>
+<PRE>
+public <B>DefaultXMLParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getXMLParser()"><!-- --></A><H3>
+getXMLParser</H3>
+<PRE>
+public org.xml.sax.XMLReader <B>getXMLParser</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html#getXMLParser()">getXMLParser</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultXMLParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html
new file mode 100644
index 0000000..3cc7e50
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+XMLBootIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLBootIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class XMLBootIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.XMLBootIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>XMLBootIdentifier</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></DL>
+
+<P>
+XMLBootIdentifier.java
+
+
+ Created: Thu May 25 11:57:19 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLBootIdentifier.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html">XMLBootIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html#XML_BOOT">XML_BOOT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdent [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XML_BOOT"><!-- --></A><H3>
+XML_BOOT</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html">XMLBootIdentifier</A> <B>XML_BOOT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html
new file mode 100644
index 0000000..15d6cb0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html
@@ -0,0 +1,280 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+XMLBootModule.MiniStack
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLBootModule.MiniStack";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootModule.MiniStack.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class XMLBootModule.MiniStack</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.XMLBootModule.MiniStack</B>
+</PRE>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>XMLBootModule.MiniStack</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#XMLBootModule.MiniStack()">XMLBootModule.MiniStack</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#peek()">peek</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#pop()">pop</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html#push(java.lang.Object)">push</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> object)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XMLBootModule.MiniStack()"><!-- --></A><H3>
+XMLBootModule.MiniStack</H3>
+<PRE>
+public <B>XMLBootModule.MiniStack</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="push(java.lang.Object)"><!-- --></A><H3>
+push</H3>
+<PRE>
+public void <B>push</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> object)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="peek()"><!-- --></A><H3>
+peek</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>peek</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="pop()"><!-- --></A><H3>
+pop</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>pop</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootModule.MiniStack.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootModule.html
new file mode 100644
index 0000000..197190d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootModule.html
@@ -0,0 +1,874 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+XMLBootModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLBootModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class XMLBootModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.XMLBootModule</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBoot.html">CinemaBoot</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>XMLBootModule</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></DL>
+
+<P>
+XMLBootModule.java
+
+ This is a module which loads other modules by parsing an XML file
+ defined by the module DTD. For itself it requires a single
+ parameter which is the file to start parsing. It can also take a
+ second parameter which defines the class to use to get the initial
+ parser instance, which should extend and override the DefaultXMLParser class.
+ The class has been written this way because at the
+ moment neither the SAX or the DOM parser API actually defines how
+ this is done and it varies from parser to parser.
+
+ Once the files have been read there is really no need to hold a
+ copy of the object structure in memory so this class uses the SAX
+ parser. Ive decided to use SAX2, which is still in beta for several
+ of the publically available parsers. Hopefully this wont be a problem.
+
+ Created: Mon May 8 20:37:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLBootModule.java,v 1.21 2002/03/08 17:44:44 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html">XMLBootModule.MiniStack</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#XMLBootModule()">XMLBootModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#characters(java.lang.String)">characters</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> chars)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#classEnd()">classEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#configStart(org.xml.sax.Attributes)">configStart</A></B>(org.xml.sax.Attributes attrib)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#enumerationEnd()">enumerationEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#fetchMainBootName()">fetchMainBootName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#fetchModuleSystemIdentifier()">fetchModuleSystemIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#genericEnd()">genericEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#getXMLParserClass()">getXMLParserClass</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#identifierStart(org.xml.sax.Attributes)">identifierStart</A></B>(org.xml.sax.Attributes attribute)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#loadEnd()">loadEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#moduleEnd()">moduleEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#nameEnd()">nameEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#nodeEnd()">nodeEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#nodeStart()">nodeStart</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#paramEnd()">paramEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#paramnameEnd()">paramnameEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#parseResource(java.lang.String, boolean)">parseResource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ boolean required)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#parseStream(java.io.InputStream)">parseStream</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> stream)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#propertiesEnd()">propertiesEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#propertiesStart()">propertiesStart</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#provideEnd()">provideEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#readEnd()">readEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#readStart(org.xml.sax.Attributes)">readStart</A></B>(org.xml.sax.Attributes attribute)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#resolveXMLLoadName(java.lang.String)">resolveXMLLoadName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#startEnd()">startEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#treeEnd()">treeEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#treeStart()">treeStart</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html#valueEnd()">valueEnd</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#fi [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XMLBootModule()"><!-- --></A><H3>
+XMLBootModule</H3>
+<PRE>
+public <B>XMLBootModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="characters(java.lang.String)"><!-- --></A><H3>
+characters</H3>
+<PRE>
+public void <B>characters</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> chars)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="classEnd()"><!-- --></A><H3>
+classEnd</H3>
+<PRE>
+public void <B>classEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="nameEnd()"><!-- --></A><H3>
+nameEnd</H3>
+<PRE>
+public void <B>nameEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paramnameEnd()"><!-- --></A><H3>
+paramnameEnd</H3>
+<PRE>
+public void <B>paramnameEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="identifierStart(org.xml.sax.Attributes)"><!-- --></A><H3>
+identifierStart</H3>
+<PRE>
+public void <B>identifierStart</B>(org.xml.sax.Attributes attribute)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="enumerationEnd()"><!-- --></A><H3>
+enumerationEnd</H3>
+<PRE>
+public void <B>enumerationEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="genericEnd()"><!-- --></A><H3>
+genericEnd</H3>
+<PRE>
+public void <B>genericEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="startEnd()"><!-- --></A><H3>
+startEnd</H3>
+<PRE>
+public void <B>startEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="loadEnd()"><!-- --></A><H3>
+loadEnd</H3>
+<PRE>
+public void <B>loadEnd</B>()
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="readStart(org.xml.sax.Attributes)"><!-- --></A><H3>
+readStart</H3>
+<PRE>
+public void <B>readStart</B>(org.xml.sax.Attributes attribute)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="readEnd()"><!-- --></A><H3>
+readEnd</H3>
+<PRE>
+public void <B>readEnd</B>()
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="valueEnd()"><!-- --></A><H3>
+valueEnd</H3>
+<PRE>
+public void <B>valueEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paramEnd()"><!-- --></A><H3>
+paramEnd</H3>
+<PRE>
+public void <B>paramEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertiesStart()"><!-- --></A><H3>
+propertiesStart</H3>
+<PRE>
+public void <B>propertiesStart</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertiesEnd()"><!-- --></A><H3>
+propertiesEnd</H3>
+<PRE>
+public void <B>propertiesEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="provideEnd()"><!-- --></A><H3>
+provideEnd</H3>
+<PRE>
+public void <B>provideEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="configStart(org.xml.sax.Attributes)"><!-- --></A><H3>
+configStart</H3>
+<PRE>
+public void <B>configStart</B>(org.xml.sax.Attributes attrib)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moduleEnd()"><!-- --></A><H3>
+moduleEnd</H3>
+<PRE>
+public void <B>moduleEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="treeStart()"><!-- --></A><H3>
+treeStart</H3>
+<PRE>
+public void <B>treeStart</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="nodeStart()"><!-- --></A><H3>
+nodeStart</H3>
+<PRE>
+public void <B>nodeStart</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="nodeEnd()"><!-- --></A><H3>
+nodeEnd</H3>
+<PRE>
+public void <B>nodeEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="treeEnd()"><!-- --></A><H3>
+treeEnd</H3>
+<PRE>
+public void <B>treeEnd</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="parseResource(java.lang.String, boolean)"><!-- --></A><H3>
+parseResource</H3>
+<PRE>
+public void <B>parseResource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ boolean required)
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="parseStream(java.io.InputStream)"><!-- --></A><H3>
+parseStream</H3>
+<PRE>
+public void <B>parseStream</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> stream)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A>,
+ org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE>
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></B></DD>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getXMLParserClass()"><!-- --></A><H3>
+getXMLParserClass</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getXMLParserClass</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fetchMainBootName()"><!-- --></A><H3>
+fetchMainBootName</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchMainBootName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fetchModuleSystemIdentifier()"><!-- --></A><H3>
+fetchModuleSystemIdentifier</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>fetchModuleSystemIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveXMLLoadName(java.lang.String)"><!-- --></A><H3>
+resolveXMLLoadName</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>resolveXMLLoadName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html
new file mode 100644
index 0000000..c0ae5a0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html
@@ -0,0 +1,574 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+XMLBootParserListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLBootParserListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootParserListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class XMLBootParserListener</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.XMLBootParserListener</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD>org.xml.sax.ContentHandler, org.xml.sax.ErrorHandler</DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>XMLBootParserListener</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements org.xml.sax.ErrorHandler, org.xml.sax.ContentHandler</DL>
+
+<P>
+XMLBootParserListener.java
+
+
+ Created: Tue May 9 22:10:53 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLBootParserListener.java,v 1.13 2001/05/08 17:46:50 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#XMLBootParserListener(uk.ac.man.bioinf.apps.xml.XMLBootModule)">XMLBootParserListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#characters(char[], int, int)">characters</A></B>(char[] ch,
+ int start,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#endDocument()">endDocument</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#endElement(java.lang.String, java.lang.String, java.lang.String)">endElement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> nameSpaceUri,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> localName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> rawName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#endPrefixMapping(java.lang.String)">endPrefixMapping</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> prefix)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#error(org.xml.sax.SAXParseException)">error</A></B>(org.xml.sax.SAXParseException param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#fatalError(org.xml.sax.SAXParseException)">fatalError</A></B>(org.xml.sax.SAXParseException param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#ignorableWhitespace(char[], int, int)">ignorableWhitespace</A></B>(char[] cha,
+ int start,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#processingInstruction(java.lang.String, java.lang.String)">processingInstruction</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> target,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> data)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#setDocumentLocator(org.xml.sax.Locator)">setDocumentLocator</A></B>(org.xml.sax.Locator locator)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#skippedEntity(java.lang.String)">skippedEntity</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#startDocument()">startDocument</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)">startElement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> nameSpaceUri,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> localName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> rawName,
+ org.xml.sax.Attributes attrib)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#startPrefixMapping(java.lang.String, java.lang.String)">startPrefixMapping</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> prefix,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> uri)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html#warning(org.xml.sax.SAXParseException)">warning</A></B>(org.xml.sax.SAXParseException param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XMLBootParserListener(uk.ac.man.bioinf.apps.xml.XMLBootModule)"><!-- --></A><H3>
+XMLBootParserListener</H3>
+<PRE>
+public <B>XMLBootParserListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html">XMLBootModule</A> mod)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setDocumentLocator(org.xml.sax.Locator)"><!-- --></A><H3>
+setDocumentLocator</H3>
+<PRE>
+public void <B>setDocumentLocator</B>(org.xml.sax.Locator locator)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>setDocumentLocator</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="startDocument()"><!-- --></A><H3>
+startDocument</H3>
+<PRE>
+public void <B>startDocument</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>startDocument</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="endDocument()"><!-- --></A><H3>
+endDocument</H3>
+<PRE>
+public void <B>endDocument</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>endDocument</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="startPrefixMapping(java.lang.String, java.lang.String)"><!-- --></A><H3>
+startPrefixMapping</H3>
+<PRE>
+public void <B>startPrefixMapping</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> prefix,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> uri)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>startPrefixMapping</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="endPrefixMapping(java.lang.String)"><!-- --></A><H3>
+endPrefixMapping</H3>
+<PRE>
+public void <B>endPrefixMapping</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> prefix)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>endPrefixMapping</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="startElement(java.lang.String, java.lang.String, java.lang.String, org.xml.sax.Attributes)"><!-- --></A><H3>
+startElement</H3>
+<PRE>
+public void <B>startElement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> nameSpaceUri,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> localName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> rawName,
+ org.xml.sax.Attributes attrib)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>startElement</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="endElement(java.lang.String, java.lang.String, java.lang.String)"><!-- --></A><H3>
+endElement</H3>
+<PRE>
+public void <B>endElement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> nameSpaceUri,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> localName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> rawName)
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>endElement</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="characters(char[], int, int)"><!-- --></A><H3>
+characters</H3>
+<PRE>
+public void <B>characters</B>(char[] ch,
+ int start,
+ int length)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>characters</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="ignorableWhitespace(char[], int, int)"><!-- --></A><H3>
+ignorableWhitespace</H3>
+<PRE>
+public void <B>ignorableWhitespace</B>(char[] cha,
+ int start,
+ int length)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>ignorableWhitespace</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="processingInstruction(java.lang.String, java.lang.String)"><!-- --></A><H3>
+processingInstruction</H3>
+<PRE>
+public void <B>processingInstruction</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> target,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> data)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>processingInstruction</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="skippedEntity(java.lang.String)"><!-- --></A><H3>
+skippedEntity</H3>
+<PRE>
+public void <B>skippedEntity</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>skippedEntity</CODE> in interface <CODE>org.xml.sax.ContentHandler</CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="error(org.xml.sax.SAXParseException)"><!-- --></A><H3>
+error</H3>
+<PRE>
+public void <B>error</B>(org.xml.sax.SAXParseException param1)
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>error</CODE> in interface <CODE>org.xml.sax.ErrorHandler</CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fatalError(org.xml.sax.SAXParseException)"><!-- --></A><H3>
+fatalError</H3>
+<PRE>
+public void <B>fatalError</B>(org.xml.sax.SAXParseException param1)
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>fatalError</CODE> in interface <CODE>org.xml.sax.ErrorHandler</CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="warning(org.xml.sax.SAXParseException)"><!-- --></A><H3>
+warning</H3>
+<PRE>
+public void <B>warning</B>(org.xml.sax.SAXParseException param1)
+ throws org.xml.sax.SAXException</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>warning</CODE> in interface <CODE>org.xml.sax.ErrorHandler</CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE>org.xml.sax.SAXException</CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLBootParserListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLModule.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLModule.html
new file mode 100644
index 0000000..c996b1e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLModule.html
@@ -0,0 +1,290 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+XMLModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Class XMLModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">uk.ac.man.bioinf.module.Module</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.XMLModule</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>XMLModule</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></DL>
+
+<P>
+XMLModule.java
+
+ This class provides configuration information specific to the
+ XMLModules. Currently there are two forms of configuration
+ information. The first is a properties file, whilst the second is
+ tree structure. These are independent and either or neither of
+ these can be present.
+
+ Created: Mon May 15 22:06:23 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLModule.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#XMLModule()">XMLModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Properties.html">Properties</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigProperties()">getConfigProperties</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html#getConfigTree()">getConfigTree</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.Module"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A>, <A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html#fi [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XMLModule()"><!-- --></A><H3>
+XMLModule</H3>
+<PRE>
+public <B>XMLModule</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getConfigProperties()"><!-- --></A><H3>
+getConfigProperties</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Properties.html">Properties</A> <B>getConfigProperties</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfigTree()"><!-- --></A><H3>
+getConfigTree</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> <B>getConfigTree</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLParserFactory.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLParserFactory.html
new file mode 100644
index 0000000..104c14a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/XMLParserFactory.html
@@ -0,0 +1,214 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:39 BST 2002 -->
+<TITLE>
+XMLParserFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLParserFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLParserFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml</FONT>
+<BR>
+Interface XMLParserFactory</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.html">CinemaXMLParserFactory</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html">DefaultXMLParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>XMLParserFactory</B></DL>
+
+<P>
+XMLParserFactory.java
+
+
+ Created: Mon Sep 18 18:52:56 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLParserFactory.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> org.xml.sax.XMLReader</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html#getXMLParser()">getXMLParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getXMLParser()"><!-- --></A><H3>
+getXMLParser</H3>
+<PRE>
+public org.xml.sax.XMLReader <B>getXMLParser</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLParserFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-frame.html
new file mode 100644
index 0000000..fbc29ab
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-frame.html
@@ -0,0 +1,53 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.xml()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.xml()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.xml</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="XMLParserFactory.html" TARGET="classFrame"><I>XMLParserFactory</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ConfigNode.html" TARGET="classFrame">ConfigNode</A>
+<BR>
+<A HREF="DefaultXMLParser.html" TARGET="classFrame">DefaultXMLParser</A>
+<BR>
+<A HREF="XMLBootIdentifier.html" TARGET="classFrame">XMLBootIdentifier</A>
+<BR>
+<A HREF="XMLBootModule.html" TARGET="classFrame">XMLBootModule</A>
+<BR>
+<A HREF="XMLBootParserListener.html" TARGET="classFrame">XMLBootParserListener</A>
+<BR>
+<A HREF="XMLModule.html" TARGET="classFrame">XMLModule</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-summary.html
new file mode 100644
index 0000000..ec2a4e0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-summary.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.xml()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.xml()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.xml
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLParserFactory.html"><I>XMLParserFactory</I></A></B></TD>
+<TD>XMLParserFactory.java
+
+
+ Created: Mon Sep 18 18:52:56 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ConfigNode.html">ConfigNode</A></B></TD>
+<TD>ConfigNode.java
+
+
+ Created: Tue May 9 21:45:13 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultXMLParser.html">DefaultXMLParser</A></B></TD>
+<TD>DefaultXMLParser.java
+
+
+ Created: Mon May 8 21:08:32 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLBootIdentifier.html">XMLBootIdentifier</A></B></TD>
+<TD>XMLBootIdentifier.java
+
+
+ Created: Thu May 25 11:57:19 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLBootModule.html">XMLBootModule</A></B></TD>
+<TD>XMLBootModule.java
+
+ This is a module which loads other modules by parsing an XML file
+ defined by the module DTD.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLBootParserListener.html">XMLBootParserListener</A></B></TD>
+<TD>XMLBootParserListener.java
+
+
+ Created: Tue May 9 22:10:53 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLModule.html">XMLModule</A></B></TD>
+<TD>XMLModule.java
+
+ This class provides configuration information specific to the
+ XMLModules.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-tree.html
new file mode 100644
index 0000000..fad6f76
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/package-tree.html
@@ -0,0 +1,146 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.xml Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.xml Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.xml
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.html"><B>XMLBootIdentifier</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html"><B>ConfigNode</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/DefaultXMLParser.html"><B>DefaultXMLParser</B></A> (implements uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html">XMLParserFactory</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.html"><B>XMLBootModule</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLModule.html"><B>XMLModule</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootModule.MiniStack.html"><B>XMLBootModule.MiniStack</B></A><LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLBootParserListener.html"><B>XMLBootParserListener</B></A> (implements org.xml.sax.ContentHandler, org.xml.sax.ErrorHandler)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.apps.xml.<A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/XMLParserFactory.html"><B>XMLParserFactory</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/systemevents/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html
new file mode 100644
index 0000000..5044fe3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+XMLLoadingTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLLoadingTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLLoadingTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml.test</FONT>
+<BR>
+Class XMLLoadingTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html">uk.ac.man.bioinf.module.NullModuleFactory</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.test.XMLLoadingTest</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>XMLLoadingTest</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A></DL>
+
+<P>
+XMLLoadingTest.java
+
+
+ Created: Tue May 16 12:35:51 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLLoadingTest.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#XMLLoadingTest()">XMLLoadingTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">addConfig</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#printNode(uk.ac.man.bioinf.apps.xml.ConfigNode)">printNode</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> node)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html#printNode(uk.ac.man.bioinf.apps.xml.ConfigNode, int)">printNode</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> node,
+ int step)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.NullModuleFactory"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#destroy()">destroy</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XMLLoadingTest()"><!-- --></A><H3>
+XMLLoadingTest</H3>
+<PRE>
+public <B>XMLLoadingTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><!-- --></A><H3>
+addConfig</H3>
+<PRE>
+public void <B>addConfig</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">addConfig</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printNode(uk.ac.man.bioinf.apps.xml.ConfigNode)"><!-- --></A><H3>
+printNode</H3>
+<PRE>
+public static void <B>printNode</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> node)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printNode(uk.ac.man.bioinf.apps.xml.ConfigNode, int)"><!-- --></A><H3>
+printNode</H3>
+<PRE>
+public static void <B>printNode</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/ConfigNode.html">ConfigNode</A> node,
+ int step)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLLoadingTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html
new file mode 100644
index 0000000..bd200c9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html
@@ -0,0 +1,254 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+XMLStartTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="XMLStartTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLStartTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.apps.xml.test</FONT>
+<BR>
+Class XMLStartTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.apps.xml.test.XMLStartTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>XMLStartTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+XMLStartTest.java
+
+
+ Created: Thu May 25 12:05:07 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: XMLStartTest.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html#XMLStartTest()">XMLStartTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="XMLStartTest()"><!-- --></A><H3>
+XMLStartTest</H3>
+<PRE>
+public <B>XMLStartTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="XMLStartTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-frame.html
new file mode 100644
index 0000000..f32f6de
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.xml.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.xml.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.apps.xml.test</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="XMLLoadingTest.html" TARGET="classFrame">XMLLoadingTest</A>
+<BR>
+<A HREF="XMLStartTest.html" TARGET="classFrame">XMLStartTest</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-summary.html
new file mode 100644
index 0000000..6294752
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-summary.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.xml.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.xml.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/database/fetch/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.apps.xml.test
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLLoadingTest.html">XMLLoadingTest</A></B></TD>
+<TD>XMLLoadingTest.java
+
+
+ Created: Tue May 16 12:35:51 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="XMLStartTest.html">XMLStartTest</A></B></TD>
+<TD>XMLStartTest.java
+
+
+ Created: Thu May 25 12:05:07 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/database/fetch/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-tree.html
new file mode 100644
index 0000000..add8ca2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/apps/xml/test/package-tree.html
@@ -0,0 +1,135 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.apps.xml.test Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.apps.xml.test Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/database/fetch/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.apps.xml.test
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html"><B>NullModuleFactory</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.test.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html"><B>XMLLoadingTest</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.apps.xml.test.<A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/test/XMLStartTest.html"><B>XMLStartTest</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/apps/xml/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/database/fetch/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html b/doc/javadoc/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html
new file mode 100644
index 0000000..aec3d19
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html
@@ -0,0 +1,358 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+ExpasySequenceRetriever
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ExpasySequenceRetriever";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ExpasySequenceRetriever.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.database.fetch</FONT>
+<BR>
+Class ExpasySequenceRetriever</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.database.fetch.ExpasySequenceRetriever</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ExpasySequenceRetriever</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A></DL>
+
+<P>
+ExpasySequenceRetriever.java
+
+ Retrieves Swissprot sequence from Expasy.
+
+ For this class to work it makes an HTTP connection, and it
+ therefore works a lot better, if the HTTP proxy has been set
+ correctly. java -DproxySet=true -DproxyHost=proxyhost
+ [-DproxyPort=portNumber] is a good way to do this.
+
+
+ It also makes explicit use of the URL format used at EXPASY, and I
+ have no idea how stable these are.
+
+ I am retrieving
+
+ Created: Thu Feb 8 17:22:05 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ExpasySequenceRetriever.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#ExpasySequenceRetriever()">ExpasySequenceRetriever</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#ExpasySequenceRetriever(java.lang.String)">ExpasySequenceRetriever</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> baseURL)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#close()">close</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#dispose()">dispose</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">retrieveSequence</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> swissprot,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html#retrieveSequenceStream(java.lang.String)">retrieveSequenceStream</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> swissprot)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ExpasySequenceRetriever()"><!-- --></A><H3>
+ExpasySequenceRetriever</H3>
+<PRE>
+public <B>ExpasySequenceRetriever</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ExpasySequenceRetriever(java.lang.String)"><!-- --></A><H3>
+ExpasySequenceRetriever</H3>
+<PRE>
+public <B>ExpasySequenceRetriever</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> baseURL)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+retrieveSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>retrieveSequence</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> swissprot,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exp)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">retrieveSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="retrieveSequenceStream(java.lang.String)"><!-- --></A><H3>
+retrieveSequenceStream</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>retrieveSequenceStream</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> swissprot)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#retrieveSequenceStream(java.lang.String)">retrieveSequenceStream</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="close()"><!-- --></A><H3>
+close</H3>
+<PRE>
+public void <B>close</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#close()">close</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="dispose()"><!-- --></A><H3>
+dispose</H3>
+<PRE>
+public void <B>dispose</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#dispose()">dispose</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ExpasySequenceRetriever.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html b/doc/javadoc/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html
new file mode 100644
index 0000000..4efdcdf
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+FetchSequenceBySwissProtID
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FetchSequenceBySwissProtID";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FetchSequenceBySwissProtID.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.database.fetch</FONT>
+<BR>
+Class FetchSequenceBySwissProtID</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.database.fetch.FetchSequenceBySwissProtID</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>FetchSequenceBySwissProtID</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+FetchSequenceBySwissProtID.java
+
+ This class fetchs a
+ Created: Wed Feb 7 14:58:40 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FetchSequenceBySwissProtID.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html#FetchSequenceBySwissProtID()">FetchSequenceBySwissProtID</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FetchSequenceBySwissProtID()"><!-- --></A><H3>
+FetchSequenceBySwissProtID</H3>
+<PRE>
+public <B>FetchSequenceBySwissProtID</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FetchSequenceBySwissProtID.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/database/fetch/SequenceRetriever.html b/doc/javadoc/uk/ac/man/bioinf/database/fetch/SequenceRetriever.html
new file mode 100644
index 0000000..35ee6f0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/database/fetch/SequenceRetriever.html
@@ -0,0 +1,281 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+SequenceRetriever
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceRetriever";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceRetriever.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.database.fetch</FONT>
+<BR>
+Interface SequenceRetriever</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html">ExpasySequenceRetriever</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceRetriever</B></DL>
+
+<P>
+SequenceRetriever.java
+
+
+ Created: Thu Feb 8 16:42:01 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceRetriever.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#close()">close</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#dispose()">dispose</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">retrieveSequence</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accession,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html#retrieveSequenceStream(java.lang.String)">retrieveSequenceStream</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accession)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="retrieveSequence(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+retrieveSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>retrieveSequence</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accession,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exp)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="retrieveSequenceStream(java.lang.String)"><!-- --></A><H3>
+retrieveSequenceStream</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> <B>retrieveSequenceStream</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accession)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="close()"><!-- --></A><H3>
+close</H3>
+<PRE>
+public void <B>close</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="dispose()"><!-- --></A><H3>
+dispose</H3>
+<PRE>
+public void <B>dispose</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceRetriever.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-frame.html
new file mode 100644
index 0000000..8eabe7b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-frame.html
@@ -0,0 +1,45 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.database.fetch()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.database.fetch()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.database.fetch</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceRetriever.html" TARGET="classFrame"><I>SequenceRetriever</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ExpasySequenceRetriever.html" TARGET="classFrame">ExpasySequenceRetriever</A>
+<BR>
+<A HREF="FetchSequenceBySwissProtID.html" TARGET="classFrame">FetchSequenceBySwissProtID</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-summary.html
new file mode 100644
index 0000000..69152c1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-summary.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.database.fetch()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.database.fetch()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.database.fetch
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceRetriever.html"><I>SequenceRetriever</I></A></B></TD>
+<TD>SequenceRetriever.java
+
+
+ Created: Thu Feb 8 16:42:01 2001</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ExpasySequenceRetriever.html">ExpasySequenceRetriever</A></B></TD>
+<TD>ExpasySequenceRetriever.java
+
+ Retrieves Swissprot sequence from Expasy.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FetchSequenceBySwissProtID.html">FetchSequenceBySwissProtID</A></B></TD>
+<TD>FetchSequenceBySwissProtID.java
+
+ This class fetchs a
+ Created: Wed Feb 7 14:58:40 2001</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-tree.html
new file mode 100644
index 0000000..e9e966c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/database/fetch/package-tree.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.database.fetch Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.database.fetch Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.database.fetch
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.database.fetch.<A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.html"><B>ExpasySequenceRetriever</B></A> (implements uk.ac.man.bioinf.database.fetch.<A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html">SequenceRetriever</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.database.fetch.<A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.html"><B>FetchSequenceBySwissProtID</B></A></UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.database.fetch.<A HREF="../../../../../../uk/ac/man/bioinf/database/fetch/SequenceRetriever.html"><B>SequenceRetriever</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/xml/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/AbstractDebug.html b/doc/javadoc/uk/ac/man/bioinf/debug/AbstractDebug.html
new file mode 100644
index 0000000..9ae16aa
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/AbstractDebug.html
@@ -0,0 +1,487 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+AbstractDebug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractDebug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Class AbstractDebug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.debug.AbstractDebug</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.DebugImpl.html">CinemaDebug.DebugImpl</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html">DefaultDebug</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html">DefaultFileDebug</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractDebug</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DL>
+
+<P>
+AbstractDebug.java
+
+
+ Created: Wed Mar 1 22:22:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD></DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#AbstractDebug()">AbstractDebug</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Object, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Object, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Object, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractDebug()"><!-- --></A><H3>
+AbstractDebug</H3>
+<PRE>
+public <B>AbstractDebug</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public abstract void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public abstract void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.Object)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.Object)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Object, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/Debug.html b/doc/javadoc/uk/ac/man/bioinf/debug/Debug.html
new file mode 100644
index 0000000..1bf0153
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/Debug.html
@@ -0,0 +1,560 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+Debug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Debug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Debug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Class Debug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.debug.Debug</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Debug</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Debug.java
+
+ This forms the basis of the Debugging architecture. All debugging
+ statements go through static methods of this class, but what is to
+ be done with these statements is delegated to an instance of
+ DebugInterface.
+
+ This instance can be set by naming the class on the command line
+ as the debug.debug property, or programmatically with the
+ setInstance() methods. If this represents a change (rather than the
+ first time the instance is set) both the old and the new instances
+ are informed what is going on, and about each other so that Debug
+ logs can be traced.
+
+ If there is a problem with the initiation of the debug class the
+ default is used, and information is dumped to System.out. What else
+ can you do under such circumstances?
+
+ Created: Wed Mar 1 21:59:20 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Debug.java,v 1.7 2001/05/08 15:50:47 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#debug">debug</A></B></CODE>
+
+<BR>
+ This is the main switch variable.</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#Debug()">Debug</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Class, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Object, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#message(java.lang.Object, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#setInstance(uk.ac.man.bioinf.debug.DebugInterface)">setInstance</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> deb)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#setInstance(java.lang.String)">setInstance</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> debugClass)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html#throwable(java.lang.Object, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="debug"><!-- --></A><H3>
+debug</H3>
+<PRE>
+public static final boolean <B>debug</B></PRE>
+<DL>
+<DD>This is the main switch variable. It if is set to true before the
+ compile then any assertions or debug statements within the code
+ will be left in place, and will impose a runtime penalty. If it
+ is set to false, before the compile then those assertions will be
+ optimised away.
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../constant-values.html#uk.ac.man.bioinf.debug.Debug.debug">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Debug()"><!-- --></A><H3>
+Debug</H3>
+<PRE>
+public <B>Debug</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setInstance(uk.ac.man.bioinf.debug.DebugInterface)"><!-- --></A><H3>
+setInstance</H3>
+<PRE>
+public static void <B>setInstance</B>(<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> deb)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInstance(java.lang.String)"><!-- --></A><H3>
+setInstance</H3>
+<PRE>
+public static void <B>setInstance</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> debugClass)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public static void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public static void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public static void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public static void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public static void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public static void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public static void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public static void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public static void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public static void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Debug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/DebugInterface.html b/doc/javadoc/uk/ac/man/bioinf/debug/DebugInterface.html
new file mode 100644
index 0000000..9fa0e5d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/DebugInterface.html
@@ -0,0 +1,413 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:40 BST 2002 -->
+<TITLE>
+DebugInterface
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DebugInterface";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DebugInterface.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Interface DebugInterface</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html">DebugMultiplexer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>DebugInterface</B></DL>
+
+<P>
+DebugInterface.java
+
+
+ Created: Wed Mar 1 22:15:41 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DebugInterface.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Object, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Object, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DebugInterface.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/DebugMultiplexer.html b/doc/javadoc/uk/ac/man/bioinf/debug/DebugMultiplexer.html
new file mode 100644
index 0000000..470150e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/DebugMultiplexer.html
@@ -0,0 +1,524 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+DebugMultiplexer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DebugMultiplexer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DebugMultiplexer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Class DebugMultiplexer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.debug.DebugMultiplexer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DebugMultiplexer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DL>
+
+<P>
+DebugMultiplexer.java
+
+ This class can be used to multiplex other DebugInterface
+ interfaces. It implements DebugInterface directly, rather than
+ extending AbstractInterface, because I want to make no assumptions
+ at all about the instances which it contains.
+
+ This class has two relevant methods public methods to install and
+ remove other DebugInterface instances. The first time install is called the
+ multiplexer automatically installs itself as the primary
+ DebugInterface instance. If all but one of its DebugInterface instances are removed
+ from it, then it will replace itself as the primary interface with
+ a DefaultDebug instance.
+
+ If any of the Debug instances fail at any time in any of their
+ methods, they will be removed. If Debug is true all of the others
+ instances will be informed of this.
+
+ Created: Sun May 7 20:49:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DebugMultiplexer.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#addDebugInstance(uk.ac.man.bioinf.debug.DebugInterface)">addDebugInstance</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> deb)</CODE>
+
+<BR>
+ Add a new Debug Interface instance.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)">both</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Class, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Object, java.lang.Object)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#message(java.lang.Object, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#removeDebugInstance(uk.ac.man.bioinf.debug.DebugInterface)">removeDebugInstance</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> deb)</CODE>
+
+<BR>
+ Remove a DebugInterface instance from the multiplexer.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html#throwable(java.lang.Object, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addDebugInstance(uk.ac.man.bioinf.debug.DebugInterface)"><!-- --></A><H3>
+addDebugInstance</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> <B>addDebugInstance</B>(<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> deb)</PRE>
+<DL>
+<DD>Add a new Debug Interface instance. This method ensures that the
+ Multiplexer is installed if it has not been so far. Note that
+ this means the old debug instance is silently replaced and junked!
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>deb</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeDebugInstance(uk.ac.man.bioinf.debug.DebugInterface)"><!-- --></A><H3>
+removeDebugInstance</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> <B>removeDebugInstance</B>(<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A> deb)</PRE>
+<DL>
+<DD>Remove a DebugInterface instance from the multiplexer.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>deb</CODE> - the interface to remove
+<DT><B>Returns:</B><DD>the interface removed. Null if the deb wasnt there</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Object, java.lang.Object)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="message(java.lang.Class, java.lang.Object)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.Object)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Object, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.String, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.String, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Object, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="both(java.lang.Class, java.lang.Object, java.lang.Throwable)"><!-- --></A><H3>
+both</H3>
+<PRE>
+public void <B>both</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> message,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DebugMultiplexer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/DefaultDebug.html b/doc/javadoc/uk/ac/man/bioinf/debug/DefaultDebug.html
new file mode 100644
index 0000000..a97cdcf
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/DefaultDebug.html
@@ -0,0 +1,296 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+DefaultDebug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultDebug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Class DefaultDebug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">uk.ac.man.bioinf.debug.AbstractDebug</A>
+ |
+ +--<B>uk.ac.man.bioinf.debug.DefaultDebug</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultDebug</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></DL>
+
+<P>
+DefaultDebug.java
+
+ Simple Debug interface which prints things to screen
+
+ Created: Thu Mar 9 17:57:34 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultDebug.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html#DefaultDebug()">DefaultDebug</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.debug.AbstractDebug"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#b [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultDebug()"><!-- --></A><H3>
+DefaultDebug</H3>
+<PRE>
+public <B>DefaultDebug</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioi [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in class <CODE><A HREF="../../../../../ [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/DefaultFileDebug.html b/doc/javadoc/uk/ac/man/bioinf/debug/DefaultFileDebug.html
new file mode 100644
index 0000000..6eb9f87
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/DefaultFileDebug.html
@@ -0,0 +1,296 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+DefaultFileDebug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultFileDebug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/NullDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultFileDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Class DefaultFileDebug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">uk.ac.man.bioinf.debug.AbstractDebug</A>
+ |
+ +--<B>uk.ac.man.bioinf.debug.DefaultFileDebug</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultFileDebug</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></DL>
+
+<P>
+DefaultFileDebug.java
+
+
+ Created: Sun May 7 23:46:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultFileDebug.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html#DefaultFileDebug(java.io.File)">DefaultFileDebug</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.debug.AbstractDebug"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#b [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultFileDebug(java.io.File)"><!-- --></A><H3>
+DefaultFileDebug</H3>
+<PRE>
+public <B>DefaultFileDebug</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioi [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in class <CODE><A HREF="../../../../../ [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/NullDebug.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultFileDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/NullDebug.html b/doc/javadoc/uk/ac/man/bioinf/debug/NullDebug.html
new file mode 100644
index 0000000..86a815f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/NullDebug.html
@@ -0,0 +1,297 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+NullDebug
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NullDebug";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.debug</FONT>
+<BR>
+Class NullDebug</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">uk.ac.man.bioinf.debug.AbstractDebug</A>
+ |
+ +--<B>uk.ac.man.bioinf.debug.NullDebug</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NullDebug</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></DL>
+
+<P>
+NullDebug.java
+
+ This class does nothing with debug methods. Very useful for
+ clearing out spam quickly!
+
+ Created: Tue May 16 12:42:54 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NullDebug.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/NullDebug.html#NullDebug()">NullDebug</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/NullDebug.html#message(java.lang.Class, java.lang.String)">message</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/debug/NullDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.debug.AbstractDebug"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html">AbstractDebug</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Class, java.lang.String, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#both(java.lang.Object, java.lang.Object, java.lang.Throwable)">both</A>, <A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#b [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NullDebug()"><!-- --></A><H3>
+NullDebug</H3>
+<PRE>
+public <B>NullDebug</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="message(java.lang.Class, java.lang.String)"><!-- --></A><H3>
+message</H3>
+<PRE>
+public void <B>message</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#message(java.lang.Class, java.lang.String)">message</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioi [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="throwable(java.lang.Class, java.lang.Throwable)"><!-- --></A><H3>
+throwable</H3>
+<PRE>
+public void <B>throwable</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> th)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A></CODE><DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html#throwable(java.lang.Class, java.lang.Throwable)">throwable</A></CODE> in class <CODE><A HREF="../../../../../ [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullDebug.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/debug/package-frame.html
new file mode 100644
index 0000000..30f7259
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/package-frame.html
@@ -0,0 +1,53 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.debug()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.debug()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../uk/ac/man/bioinf/debug/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.debug</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="DebugInterface.html" TARGET="classFrame"><I>DebugInterface</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractDebug.html" TARGET="classFrame">AbstractDebug</A>
+<BR>
+<A HREF="Debug.html" TARGET="classFrame">Debug</A>
+<BR>
+<A HREF="DebugMultiplexer.html" TARGET="classFrame">DebugMultiplexer</A>
+<BR>
+<A HREF="DefaultDebug.html" TARGET="classFrame">DefaultDebug</A>
+<BR>
+<A HREF="DefaultFileDebug.html" TARGET="classFrame">DefaultFileDebug</A>
+<BR>
+<A HREF="NullDebug.html" TARGET="classFrame">NullDebug</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/debug/package-summary.html
new file mode 100644
index 0000000..46d6363
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/package-summary.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.debug()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.debug()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/database/fetch/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/color/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.debug
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DebugInterface.html"><I>DebugInterface</I></A></B></TD>
+<TD>DebugInterface.java
+
+
+ Created: Wed Mar 1 22:15:41 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractDebug.html">AbstractDebug</A></B></TD>
+<TD>AbstractDebug.java
+
+
+ Created: Wed Mar 1 22:22:22 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Debug.html">Debug</A></B></TD>
+<TD>Debug.java
+
+ This forms the basis of the Debugging architecture.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DebugMultiplexer.html">DebugMultiplexer</A></B></TD>
+<TD>DebugMultiplexer.java
+
+ This class can be used to multiplex other DebugInterface
+ interfaces.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultDebug.html">DefaultDebug</A></B></TD>
+<TD>DefaultDebug.java
+
+ Simple Debug interface which prints things to screen
+
+ Created: Thu Mar 9 17:57:34 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultFileDebug.html">DefaultFileDebug</A></B></TD>
+<TD>DefaultFileDebug.java
+
+
+ Created: Sun May 7 23:46:57 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NullDebug.html">NullDebug</A></B></TD>
+<TD>NullDebug.java
+
+ This class does nothing with debug methods.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/database/fetch/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/color/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/debug/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/debug/package-tree.html
new file mode 100644
index 0000000..46e564b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/debug/package-tree.html
@@ -0,0 +1,141 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.debug Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.debug Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/database/fetch/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/color/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.debug
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/AbstractDebug.html"><B>AbstractDebug</B></A> (implements uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultDebug.html"><B>DefaultDebug</B></A><LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/DefaultFileDebug.html"><B>DefaultFileDebug</B></A><LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/NullDebug.html"><B>NullDebug</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/Debug.html"><B>Debug</B></A><LI TYPE="circle">class uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugMultiplexer.html"><B>DebugMultiplexer</B></A> (implements uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html">DebugInterface</A>)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.debug.<A HREF="../../../../../uk/ac/man/bioinf/debug/DebugInterface.html"><B>DebugInterface</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/database/fetch/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/color/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorGenerator.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorGenerator.html
new file mode 100644
index 0000000..d713302
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorGenerator.html
@@ -0,0 +1,306 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+ColorGenerator
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorGenerator";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorGenerator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class ColorGenerator</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.ColorGenerator</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ColorGenerator</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ColorGenerator.java
+
+ This class generates a stream of colours, cycling through all of
+ the colours in the list until it has finished.
+
+ Created: Wed May 24 09:54:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorGenerator.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html#ColorGenerator()">ColorGenerator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html#ColorGenerator(java.awt.Color[])">ColorGenerator</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] colors)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html#getAllColorGenerator()">getAllColorGenerator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html#getLightColorGenerator()">getLightColorGenerator</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html#next()">next</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ColorGenerator()"><!-- --></A><H3>
+ColorGenerator</H3>
+<PRE>
+public <B>ColorGenerator</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ColorGenerator(java.awt.Color[])"><!-- --></A><H3>
+ColorGenerator</H3>
+<PRE>
+public <B>ColorGenerator</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] colors)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAllColorGenerator()"><!-- --></A><H3>
+getAllColorGenerator</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A> <B>getAllColorGenerator</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLightColorGenerator()"><!-- --></A><H3>
+getLightColorGenerator</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html">ColorGenerator</A> <B>getLightColorGenerator</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="next()"><!-- --></A><H3>
+next</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>next</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorGenerator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorList.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorList.html
new file mode 100644
index 0000000..9559a50
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorList.html
@@ -0,0 +1,413 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+ColorList
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorList";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorStore.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class ColorList</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.ColorList</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ColorList</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ColorList.java
+
+ This class is similar to ColorGenerator, except that instead of
+ cycling through the colours it presents them as a list
+
+ Created: Thu Jun 8 17:37:23 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorList.java,v 1.3 2002/03/08 14:52:36 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#colors">colors</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#ColorList()">ColorList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#ColorList(java.awt.Color[])">ColorList</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] colors)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#getAllColorList()">getAllColorList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#getColdToHotColorList()">getColdToHotColorList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#getColorAt(int)">getColorAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#getGray50List()">getGray50List</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#getHotToColdColorList()">getHotToColdColorList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#getLightColorList()">getLightColorList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html#length()">length</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="colors"><!-- --></A><H3>
+colors</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] <B>colors</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ColorList()"><!-- --></A><H3>
+ColorList</H3>
+<PRE>
+public <B>ColorList</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ColorList(java.awt.Color[])"><!-- --></A><H3>
+ColorList</H3>
+<PRE>
+public <B>ColorList</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] colors)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(int)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="length()"><!-- --></A><H3>
+length</H3>
+<PRE>
+public int <B>length</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAllColorList()"><!-- --></A><H3>
+getAllColorList</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> <B>getAllColorList</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLightColorList()"><!-- --></A><H3>
+getLightColorList</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> <B>getLightColorList</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColdToHotColorList()"><!-- --></A><H3>
+getColdToHotColorList</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> <B>getColdToHotColorList</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getHotToColdColorList()"><!-- --></A><H3>
+getHotToColdColorList</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> <B>getHotToColdColorList</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGray50List()"><!-- --></A><H3>
+getGray50List</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> <B>getGray50List</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorStore.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorMap.html
new file mode 100644
index 0000000..6f7de3f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorMap.html
@@ -0,0 +1,250 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+ColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Interface ColorMap</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html">DoubleArrayColorMap</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html">IndividualElementColorMap</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">Perc [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ColorMap</B></DL>
+
+<P>
+ColorMap.java
+
+ The interface to support color mapping of elements in a sequence
+ alignment. NB: Objects of this type should be immutable.
+
+ Created: Thu Mar 23 18:32:32 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorMap.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the Color at a specific position in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this colour scheme.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Returns the Color at a specific position in the alignment. This
+ method will do various things depending on the actual color map
+ implemented.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>elem</CODE> - the element<DD><CODE>point</CODE> - the location within the SA
+<DT><B>Returns:</B><DD>the color</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD>Returns the name of this colour scheme.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorMapException.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorMapException.html
new file mode 100644
index 0000000..ed19513
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorMapException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+ColorMapException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorMapException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorMapException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class ColorMapException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.ColorMapException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ColorMapException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+ColorMapException.java
+
+
+ Created: Mon Apr 10 09:06:32 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorMapException.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.color.ColorMapException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMapException.html#ColorMapException(java.lang.String)">ColorMapException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ColorMapException(java.lang.String)"><!-- --></A><H3>
+ColorMapException</H3>
+<PRE>
+public <B>ColorMapException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorMapException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorStore.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorStore.html
new file mode 100644
index 0000000..c954f15
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ColorStore.html
@@ -0,0 +1,194 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+ColorStore
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorStore";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorStore.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class ColorStore</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.ColorStore</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ColorStore</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ColorStore.java
+
+ This is a static place holder of various lists of colours.
+
+ Created: Thu Jun 8 17:39:09 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorStore.java,v 1.4 2002/03/08 15:04:45 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorStore.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#methods_inherited_from_class_java.lang.Object">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html
new file mode 100644
index 0000000..de885e4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+DoubleArrayColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DoubleArrayColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorStore.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DoubleArrayColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class DoubleArrayColorMap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.DoubleArrayColorMap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DoubleArrayColorMap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DL>
+
+<P>
+DoubleArrayColorMap.java
+
+ This class takes a series of doubles, a list of colours and a
+ sequence alignment and turns them into a colour map.
+
+ The list of doubles is a colour for every element in every
+ sequence. Numbering starts at 0, and DOES NOT include gaps. Hence
+ element 0,0 of the array is the first element of the first sequence
+ where ever it starts.
+
+ Created: Thu Jun 21 16:42:36 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DoubleArrayColorMap.java,v 1.1 2002/03/08 14:53:36 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html#DoubleArrayColorMap(double[][], uk.ac.man.bioinf.gui.color.ColorList)">DoubleArrayColorMap</A></B>(double[][] array,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> colors)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the Color at a specific position in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this colour scheme.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DoubleArrayColorMap(double[][], uk.ac.man.bioinf.gui.color.ColorList)"><!-- --></A><H3>
+DoubleArrayColorMap</H3>
+<PRE>
+public <B>DoubleArrayColorMap</B>(double[][] array,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> colors)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the Color at a specific position in the alignment. This
+ method will do various things depending on the actual color map
+ implemented.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>elem</CODE> - the element<DD><CODE>point</CODE> - the location within the SA
+<DT><B>Returns:</B><DD>the color</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the name of this colour scheme.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorStore.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DoubleArrayColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html
new file mode 100644
index 0000000..1945a63
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+IndividualElementColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="IndividualElementColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IndividualElementColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class IndividualElementColorMap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.IndividualElementColorMap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>IndividualElementColorMap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DL>
+
+<P>
+IndividualElementColorMap.java
+
+ Allows a direct mapping between an element and a color; thereby
+ every element in a sequence type will have an associated color.
+ NB: This class is <b>NOT</b> synchronized.
+
+ Created: Thu Apr 6 13:13:24 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: IndividualElementColorMap.java,v 1.8 2001/07/06 11:52:51 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html#IndividualElementColorMap(java.lang.String, uk.ac.man.bioinf.sequence.Element[], java.awt.Color[])">IndividualElementColorMap</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] colors)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the color for an element at a specific position in the
+ alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this color map.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IndividualElementColorMap(java.lang.String, uk.ac.man.bioinf.sequence.Element[], java.awt.Color[])"><!-- --></A><H3>
+IndividualElementColorMap</H3>
+<PRE>
+public <B>IndividualElementColorMap</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A>[] colors)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Returns the color for an element at a specific position in the
+ alignment. [from ColorMap] NB: In this case, this simply
+ identifies the element and returns the color for that element.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>element</CODE> - the element from the position in the SA<DD><CODE>point</CODE> - the position in the SA
+<DT><B>Returns:</B><DD>the color of the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD>Returns the name of this color map.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the color map name</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IndividualElementColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html
new file mode 100644
index 0000000..4a63160
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html
@@ -0,0 +1,364 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+PercentIDVarianceColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PercentIDVarianceColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentIDVarianceColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class PercentIDVarianceColorMap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PercentIDVarianceColorMap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A></DL>
+
+<P>
+PercentIDVarianceColorMap.java
+
+ Calculates a colour scheme
+
+ Created: Fri Jun 9 16:03:46 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PercentIDVarianceColorMap.java,v 1.10 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#PercentIDVarianceColorMap(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator)">PercentIDVarianceColorMap</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> calculator)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#PercentIDVarianceColorMap(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator, uk.ac.man.bioinf.gui.color.ColorList)">PercentIDVarianceColorMap</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> calculator,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> lowToHighColours)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#calculate()">calculate</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the Color at a specific position in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this colour scheme.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PercentIDVarianceColorMap(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator)"><!-- --></A><H3>
+PercentIDVarianceColorMap</H3>
+<PRE>
+public <B>PercentIDVarianceColorMap</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> calculator)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="PercentIDVarianceColorMap(uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator, uk.ac.man.bioinf.gui.color.ColorList)"><!-- --></A><H3>
+PercentIDVarianceColorMap</H3>
+<PRE>
+public <B>PercentIDVarianceColorMap</B>(<A HREF="../../../../../../uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.html">PercentageIDCalculator</A> calculator,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html">ColorList</A> lowToHighColours)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the Color at a specific position in the alignment. This
+ method will do various things depending on the actual color map
+ implemented.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>elem</CODE> - the element<DD><CODE>point</CODE> - the location within the SA
+<DT><B>Returns:</B><DD>the color</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the name of this colour scheme.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calculate()"><!-- --></A><H3>
+calculate</H3>
+<PRE>
+public void <B>calculate</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html#calculate()">calculate</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PercentIDVarianceColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/SingleColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/SingleColorMap.html
new file mode 100644
index 0000000..3e6c2ec
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/SingleColorMap.html
@@ -0,0 +1,313 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+SingleColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SingleColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class SingleColorMap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.SingleColorMap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SingleColorMap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DL>
+
+<P>
+SingleColorMap.java
+
+ This class is designed to return one color, regardless of the
+ element being displayed. Thus, this is able to provide no color
+ scheme, by being set to the background color at run time.
+
+ Created: Tue Apr 11 17:42:19 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SingleColorMap.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html#SingleColorMap(java.awt.Color)">SingleColorMap</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html#SingleColorMap(java.awt.Color, java.lang.String)">SingleColorMap</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the Color at a specific position in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this colour scheme.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SingleColorMap(java.awt.Color)"><!-- --></A><H3>
+SingleColorMap</H3>
+<PRE>
+public <B>SingleColorMap</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SingleColorMap(java.awt.Color, java.lang.String)"><!-- --></A><H3>
+SingleColorMap</H3>
+<PRE>
+public <B>SingleColorMap</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the Color at a specific position in the alignment. This
+ method will do various things depending on the actual color map
+ implemented.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>element</CODE> - the element<DD><CODE>point</CODE> - the location within the SA
+<DT><B>Returns:</B><DD>the color</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the name of this colour scheme.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ThreadableColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ThreadableColorMap.html
new file mode 100644
index 0000000..fa09d85
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ThreadableColorMap.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:41 BST 2002 -->
+<TITLE>
+ThreadableColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ThreadableColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadableColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Interface ThreadableColorMap</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ThreadableColorMap</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></DL>
+
+<P>
+ThreadableColorMap.java
+
+ Defines a color map that can perform any necessary calculations to
+ in a thread safe manner. The class is not required to perform the
+ threading, but it is required to perform the calculation in a
+ thread safe way. In other words the getColorAt() method should
+ function safely even whilst calculate method is being called.
+
+ Created: Fri Dec 1 14:45:34 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ThreadableColorMap.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html#calculate()">calculate</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.color.ColorMap"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="calculate()"><!-- --></A><H3>
+calculate</H3>
+<PRE>
+public void <B>calculate</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadableColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/ThreadedColorMap.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/ThreadedColorMap.html
new file mode 100644
index 0000000..0e514d4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/ThreadedColorMap.html
@@ -0,0 +1,495 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+ThreadedColorMap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ThreadedColorMap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.color</FONT>
+<BR>
+Class ThreadedColorMap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.color.ThreadedColorMap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>, <A HREF="../../../../.. [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ThreadedColorMap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/produ [...]
+
+<P>
+ThreadedColorMap.java
+
+ This class implements the threaded functionality for ColorMap. You
+ can use this class to wrap up any other ThreadableColorMap and it
+ will take care of the out thread calculation.
+
+ This class it should be noted is immutable in the sense that the
+ SequenceAlignment it set in the constructor, and you can not change
+ this, so you will need to create a new object.
+
+
+ Created: Fri Dec 1 14:58:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ThreadedColorMap.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#NAME">NAME</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#ThreadedColorMap(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.color.ThreadableColorMap)">ThreadedColorMap</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A> map)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#ThreadedColorMap(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.color.ThreadableColorMap, uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)">ThreadedColorMap</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A> map,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> queue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Returns the Color at a specific position in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#getInternalThreadedColorMap()">getInternalThreadedColorMap</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the name of this colour scheme.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html#validate()">validate</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NAME"><!-- --></A><H3>
+NAME</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>NAME</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.gui.color.ThreadedColorMap.NAME">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ThreadedColorMap(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.color.ThreadableColorMap)"><!-- --></A><H3>
+ThreadedColorMap</H3>
+<PRE>
+public <B>ThreadedColorMap</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A> map)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ThreadedColorMap(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.gui.color.ThreadableColorMap, uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue)"><!-- --></A><H3>
+ThreadedColorMap</H3>
+<PRE>
+public <B>ThreadedColorMap</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A> map,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.html">InvokerInternalQueue</A> queue)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getColorAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getColorAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the Color at a specific position in the alignment. This
+ method will do various things depending on the actual color map
+ implemented.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getColorAt(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getColorAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> - the sequence alignment<DD><CODE>element</CODE> - the element<DD><CODE>point</CODE> - the location within the SA
+<DT><B>Returns:</B><DD>the color</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="validate()"><!-- --></A><H3>
+validate</H3>
+<PRE>
+protected void <B>validate</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></B></DD>
+<DD>Returns the name of this colour scheme.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInternalThreadedColorMap()"><!-- --></A><H3>
+getInternalThreadedColorMap</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getInternalThreadedColorMap</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ThreadedColorMap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/package-frame.html
new file mode 100644
index 0000000..562cdee
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/package-frame.html
@@ -0,0 +1,70 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.color()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.color()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.color</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ColorMap.html" TARGET="classFrame"><I>ColorMap</I></A>
+<BR>
+<A HREF="ThreadableColorMap.html" TARGET="classFrame"><I>ThreadableColorMap</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ColorGenerator.html" TARGET="classFrame">ColorGenerator</A>
+<BR>
+<A HREF="ColorList.html" TARGET="classFrame">ColorList</A>
+<BR>
+<A HREF="ColorStore.html" TARGET="classFrame">ColorStore</A>
+<BR>
+<A HREF="DoubleArrayColorMap.html" TARGET="classFrame">DoubleArrayColorMap</A>
+<BR>
+<A HREF="IndividualElementColorMap.html" TARGET="classFrame">IndividualElementColorMap</A>
+<BR>
+<A HREF="PercentIDVarianceColorMap.html" TARGET="classFrame">PercentIDVarianceColorMap</A>
+<BR>
+<A HREF="SingleColorMap.html" TARGET="classFrame">SingleColorMap</A>
+<BR>
+<A HREF="ThreadedColorMap.html" TARGET="classFrame">ThreadedColorMap</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ColorMapException.html" TARGET="classFrame">ColorMapException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/package-summary.html
new file mode 100644
index 0000000..613967a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/package-summary.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:10 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.color()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.color()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.color
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorMap.html"><I>ColorMap</I></A></B></TD>
+<TD>ColorMap.java
+
+ The interface to support color mapping of elements in a sequence
+ alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ThreadableColorMap.html"><I>ThreadableColorMap</I></A></B></TD>
+<TD>ThreadableColorMap.java
+
+ Defines a color map that can perform any necessary calculations to
+ in a thread safe manner.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorGenerator.html">ColorGenerator</A></B></TD>
+<TD>ColorGenerator.java
+
+ This class generates a stream of colours, cycling through all of
+ the colours in the list until it has finished.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorList.html">ColorList</A></B></TD>
+<TD>ColorList.java
+
+ This class is similar to ColorGenerator, except that instead of
+ cycling through the colours it presents them as a list
+
+ Created: Thu Jun 8 17:37:23 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorStore.html">ColorStore</A></B></TD>
+<TD>ColorStore.java
+
+ This is a static place holder of various lists of colours.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DoubleArrayColorMap.html">DoubleArrayColorMap</A></B></TD>
+<TD>DoubleArrayColorMap.java
+
+ This class takes a series of doubles, a list of colours and a
+ sequence alignment and turns them into a colour map.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="IndividualElementColorMap.html">IndividualElementColorMap</A></B></TD>
+<TD>IndividualElementColorMap.java
+
+ Allows a direct mapping between an element and a color; thereby
+ every element in a sequence type will have an associated color.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PercentIDVarianceColorMap.html">PercentIDVarianceColorMap</A></B></TD>
+<TD>PercentIDVarianceColorMap.java
+
+ Calculates a colour scheme
+
+ Created: Fri Jun 9 16:03:46 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SingleColorMap.html">SingleColorMap</A></B></TD>
+<TD>SingleColorMap.java
+
+ This class is designed to return one color, regardless of the
+ element being displayed.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ThreadedColorMap.html">ThreadedColorMap</A></B></TD>
+<TD>ThreadedColorMap.java
+
+ This class implements the threaded functionality for ColorMap.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorMapException.html">ColorMapException</A></B></TD>
+<TD>ColorMapException.java
+
+
+ Created: Mon Apr 10 09:06:32 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/color/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/color/package-tree.html
new file mode 100644
index 0000000..a6ff2fb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/color/package-tree.html
@@ -0,0 +1,151 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.color Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.color Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.color
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorGenerator.html"><B>ColorGenerator</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorList.html"><B>ColorList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorStore.html"><B>ColorStore</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HRE [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/IndividualElementColorMap.html"><B>IndividualElementColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.html"><B>PercentIDVarianceColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html">ThreadableColorMap</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/SingleColorMap.html"><B>SingleColorMap</B></A> (implements uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadedColorMap.html"><B>ThreadedColorMap</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2 [...]
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMapException.html"><B>ColorMapException</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html"><B>ColorMap</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.gui.color.<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ThreadableColorMap.html"><B>ThreadableColorMap</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/debug/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/misc/ChunkyListModel.html b/doc/javadoc/uk/ac/man/bioinf/gui/misc/ChunkyListModel.html
new file mode 100644
index 0000000..e5df4e5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/misc/ChunkyListModel.html
@@ -0,0 +1,1054 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:42 BST 2002 -->
+<TITLE>
+ChunkyListModel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ChunkyListModel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChunkyListModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_javax.swing.AbstractListModel">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.misc</FONT>
+<BR>
+Class ChunkyListModel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">javax.swing.AbstractListModel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.misc.ChunkyListModel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ChunkyListModel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">AbstractListModel</A></DL>
+
+<P>
+ChunkyListModel.java
+
+ This is a small extension to the list model class. It allows the addition
+ of several elements at once, with only one fireIntervalAdded event occuring.
+ The reason for this is essentially performance. The DefaultListModel appears
+ to cause a huge amount of repainting whilst it is being loaded with data, which
+ means that it gets a lot slower to add elements when they already are. Whilst there
+ are probably better ways to solve this problem, the simplest would appear to be
+ add the elements in chunks.
+
+ Since I have written this code I have found various other ways
+ around the repaint problem. However this code is still pretty
+ useful because its got some nice convenience methods for adding and
+ removing many elements at once.
+
+ The class name is still pretty terrible though.
+
+ <P>
+ Created: Tue Nov 17 13:43:56 1998
+ <P>
+ Compliant: 1.0
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ChunkyListModel.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.misc.ChunkyListModel">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.AbstractListModel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">AbstractListModel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#listenerList">listenerList</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#ChunkyListModel()">ChunkyListModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#add(int, java.lang.Object)">add</A></B>(int index,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addAll(java.util.Collection)">addAll</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Collection.html">Collection</A> collection)</CODE>
+
+<BR>
+ This method takes a collection, adds all the elements,
+ then fires an event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addAll(java.lang.Object[])">addAll</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] object)</CODE>
+
+<BR>
+ Add all the elements of this array to the list model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addAll(java.util.Vector)">addAll</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Vector.html">Vector</A> vector)</CODE>
+
+<BR>
+ Add all the elements of this vector to the list model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#addElement(java.lang.Object)">addElement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#capacity()">capacity</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#clear()">clear</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#contains(java.lang.Object)">contains</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#copyInto(java.lang.Object[])">copyInto</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] anArray)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#elementAt(int)">elementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Enumeration.html">Enumeration</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#elements()">elements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#ensureCapacity(int)">ensureCapacity</A></B>(int minCapacity)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#firstElement()">firstElement</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#get(int)">get</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#getSize()">getSize</A></B>()</CODE>
+
+<BR>
+ Everything that follows this is just a straight copy from
+ the default list model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#indexOf(java.lang.Object)">indexOf</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#indexOf(java.lang.Object, int)">indexOf</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#insertElementAt(java.lang.Object, int)">insertElementAt</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#isEmpty()">isEmpty</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#lastElement()">lastElement</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#lastIndexOf(java.lang.Object)">lastIndexOf</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#lastIndexOf(java.lang.Object, int)">lastIndexOf</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#remove(int)">remove</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAll(java.util.Collection)">removeAll</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Collection.html">Collection</A> collection)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAll(java.lang.Object[])">removeAll</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] object)</CODE>
+
+<BR>
+ Removes all the elements of this array from the list modely</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAll(java.util.Vector)">removeAll</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Vector.html">Vector</A> vector)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeAllElements()">removeAllElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeElement(java.lang.Object)">removeElement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeElementAt(int)">removeElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#removeRange(int, int)">removeRange</A></B>(int fromIndex,
+ int toIndex)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#set(int, java.lang.Object)">set</A></B>(int index,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#setElementAt(java.lang.Object, int)">setElementAt</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#setSize(int)">setSize</A></B>(int newSize)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#size()">size</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#toArray()">toArray</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#toList()">toList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html#trimToSize()">trimToSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.AbstractListModel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html">AbstractListModel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#addListDataListener(javax.swing.event.ListDataListener)">addListDataListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#fireContentsChanged(java.lang.Object, int, int)">fireContentsChanged</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html#fireIntervalAdded(java.lang.Object, int, int)">fireInter [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ChunkyListModel()"><!-- --></A><H3>
+ChunkyListModel</H3>
+<PRE>
+public <B>ChunkyListModel</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addAll(java.util.Collection)"><!-- --></A><H3>
+addAll</H3>
+<PRE>
+public void <B>addAll</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Collection.html">Collection</A> collection)</PRE>
+<DL>
+<DD>This method takes a collection, adds all the elements,
+ then fires an event. This method isnt thread safe, call
+ from the event thread only
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAll(java.lang.Object[])"><!-- --></A><H3>
+addAll</H3>
+<PRE>
+public void <B>addAll</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] object)</PRE>
+<DL>
+<DD>Add all the elements of this array to the list model
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>object</CODE> - the array</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAll(java.util.Vector)"><!-- --></A><H3>
+addAll</H3>
+<PRE>
+public void <B>addAll</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Vector.html">Vector</A> vector)</PRE>
+<DL>
+<DD>Add all the elements of this vector to the list model
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>vector</CODE> - the vector</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toList()"><!-- --></A><H3>
+toList</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> <B>toList</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAll(java.lang.Object[])"><!-- --></A><H3>
+removeAll</H3>
+<PRE>
+public void <B>removeAll</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] object)</PRE>
+<DL>
+<DD>Removes all the elements of this array from the list modely
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>object</CODE> - the array</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAll(java.util.Vector)"><!-- --></A><H3>
+removeAll</H3>
+<PRE>
+public void <B>removeAll</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Vector.html">Vector</A> vector)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAll(java.util.Collection)"><!-- --></A><H3>
+removeAll</H3>
+<PRE>
+public void <B>removeAll</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Collection.html">Collection</A> collection)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSize()"><!-- --></A><H3>
+getSize</H3>
+<PRE>
+public int <B>getSize</B>()</PRE>
+<DL>
+<DD>Everything that follows this is just a straight copy from
+ the default list model
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the size</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="copyInto(java.lang.Object[])"><!-- --></A><H3>
+copyInto</H3>
+<PRE>
+public void <B>copyInto</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] anArray)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="trimToSize()"><!-- --></A><H3>
+trimToSize</H3>
+<PRE>
+public void <B>trimToSize</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="ensureCapacity(int)"><!-- --></A><H3>
+ensureCapacity</H3>
+<PRE>
+public void <B>ensureCapacity</B>(int minCapacity)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSize(int)"><!-- --></A><H3>
+setSize</H3>
+<PRE>
+public void <B>setSize</B>(int newSize)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="capacity()"><!-- --></A><H3>
+capacity</H3>
+<PRE>
+public int <B>capacity</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isEmpty()"><!-- --></A><H3>
+isEmpty</H3>
+<PRE>
+public boolean <B>isEmpty</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="elements()"><!-- --></A><H3>
+elements</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Enumeration.html">Enumeration</A> <B>elements</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="contains(java.lang.Object)"><!-- --></A><H3>
+contains</H3>
+<PRE>
+public boolean <B>contains</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="indexOf(java.lang.Object)"><!-- --></A><H3>
+indexOf</H3>
+<PRE>
+public int <B>indexOf</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="indexOf(java.lang.Object, int)"><!-- --></A><H3>
+indexOf</H3>
+<PRE>
+public int <B>indexOf</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="lastIndexOf(java.lang.Object)"><!-- --></A><H3>
+lastIndexOf</H3>
+<PRE>
+public int <B>lastIndexOf</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="lastIndexOf(java.lang.Object, int)"><!-- --></A><H3>
+lastIndexOf</H3>
+<PRE>
+public int <B>lastIndexOf</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="elementAt(int)"><!-- --></A><H3>
+elementAt</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>elementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firstElement()"><!-- --></A><H3>
+firstElement</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>firstElement</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="lastElement()"><!-- --></A><H3>
+lastElement</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>lastElement</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAt(java.lang.Object, int)"><!-- --></A><H3>
+setElementAt</H3>
+<PRE>
+public void <B>setElementAt</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeElementAt(int)"><!-- --></A><H3>
+removeElementAt</H3>
+<PRE>
+public void <B>removeElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAt(java.lang.Object, int)"><!-- --></A><H3>
+insertElementAt</H3>
+<PRE>
+public void <B>insertElementAt</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addElement(java.lang.Object)"><!-- --></A><H3>
+addElement</H3>
+<PRE>
+public void <B>addElement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeElement(java.lang.Object)"><!-- --></A><H3>
+removeElement</H3>
+<PRE>
+public boolean <B>removeElement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAllElements()"><!-- --></A><H3>
+removeAllElements</H3>
+<PRE>
+public void <B>removeAllElements</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toArray()"><!-- --></A><H3>
+toArray</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] <B>toArray</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="get(int)"><!-- --></A><H3>
+get</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>get</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="set(int, java.lang.Object)"><!-- --></A><H3>
+set</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>set</B>(int index,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> element)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="add(int, java.lang.Object)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public void <B>add</B>(int index,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> element)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(int)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>remove</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clear()"><!-- --></A><H3>
+clear</H3>
+<PRE>
+public void <B>clear</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeRange(int, int)"><!-- --></A><H3>
+removeRange</H3>
+<PRE>
+public void <B>removeRange</B>(int fromIndex,
+ int toIndex)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChunkyListModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_javax.swing.AbstractListModel">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html b/doc/javadoc/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html
new file mode 100644
index 0000000..e828b64
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html
@@ -0,0 +1,302 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:43 BST 2002 -->
+<TITLE>
+SwappingListBasicUI.SwappingMouseInputHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SwappingListBasicUI.SwappingMouseInputHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SwappingListBasicUI.SwappingMouseInputHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.misc</FONT>
+<BR>
+Class SwappingListBasicUI.SwappingMouseInputHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html">javax.swing.plaf.basic.BasicListUI.MouseInputHandler</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.misc.SwappingListBasicUI.SwappingMouseInputHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseMotionListener.html">MouseMotionListene [...]
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html">SwappingListBasicUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SwappingListBasicUI.SwappingMouseInputHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html">BasicListUI.MouseInputHandler</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#SwappingListBasicUI.SwappingMouseInputHandler()">SwappingListBasicUI.SwappingMouseInputHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#mouseDragged(java.awt.event.MouseEvent)">mouseDragged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#mousePressed(java.awt.event.MouseEvent)">mousePressed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html#swap(int, int)">swap</A></B>(int max,
+ int min)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.basic.BasicListUI.MouseInputHandler"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html">BasicListUI.MouseInputHandler</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html#mouseClicked(java.awt.event.MouseEvent)">mouseClicked</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html#mouseEntered(java.awt.event.MouseEvent)">mouseEntered</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html#mouseExited(java.awt.even [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SwappingListBasicUI.SwappingMouseInputHandler()"><!-- --></A><H3>
+SwappingListBasicUI.SwappingMouseInputHandler</H3>
+<PRE>
+public <B>SwappingListBasicUI.SwappingMouseInputHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="mousePressed(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mousePressed</H3>
+<PRE>
+public void <B>mousePressed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mousePressed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html#mousePressed(java.awt.event.MouseEvent)">mousePressed</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/Bas [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseDragged(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseDragged</H3>
+<PRE>
+public void <B>mouseDragged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseDragged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseMotionListener.html">MouseMotionListener</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html#mouseDragged(java.awt.event.MouseEvent)">mouseDragged</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/pl [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="swap(int, int)"><!-- --></A><H3>
+swap</H3>
+<PRE>
+protected void <B>swap</B>(int max,
+ int min)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SwappingListBasicUI.SwappingMouseInputHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html b/doc/javadoc/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html
new file mode 100644
index 0000000..745629f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html
@@ -0,0 +1,368 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:43 BST 2002 -->
+<TITLE>
+SwappingListBasicUI
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SwappingListBasicUI";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SwappingListBasicUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.plaf.basic.BasicListUI">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.misc</FONT>
+<BR>
+Class SwappingListBasicUI</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">javax.swing.plaf.ComponentUI</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ListUI.html">javax.swing.plaf.ListUI</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">javax.swing.plaf.basic.BasicListUI</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.misc.SwappingListBasicUI</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SwappingListBasicUI</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">BasicListUI</A></DL>
+
+<P>
+SwappingListBasicUI.java
+
+ This class enables dragging of list items around something like
+ XMMS's playlist.
+ Because it has to modify the list it must perform a dodgy cast, to
+ some form of modifiable ListModel. In this case it assumes that the
+ list extends DefaultListModel. (PENDING:- PL) I should include some
+ checking for this when ever the UI is associated with a JList or
+ whenever the ListModel is changed, which would give me fail fast
+ behaviour.
+
+ Created: Tue Oct 3 18:40:07 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SwappingListBasicUI.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html">SwappingListBasicUI.SwappingMouseInputHandler</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.plaf.basic.BasicListUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">BasicListUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.FocusHandler.html">BasicListUI.FocusHandler</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.ListDataHandler.html">BasicListUI.ListDataHandler</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.ListSelectionHandler.html">BasicListUI.ListSelectionHandler</A>, <A HREF="http://java.sun.com/products/jdk/1 [...]
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.plaf.basic.BasicListUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">BasicListUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#cellHeight">cellHeight</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#cellHeights">cellHeights</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#cellRendererChanged">cellRendererChanged</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.htm [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#SwappingListBasicUI()">SwappingListBasicUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#convertYToRow(int)">convertYToRow</A></B>(int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#createMouseInputListener()">createMouseInputListener</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html#getJList()">getJList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.basic.BasicListUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">BasicListUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#convertRowToY(int)">convertRowToY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#createFocusListener()">createFocusListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#createListDataListener()">createListDataListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/j [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.ComponentUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#contains(javax.swing.JComponent, int, int)">contains</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChild(javax.swing.JComponent, int)">getAccessibleChild</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChildrenCount(javax.swing.JComponent)">getAccessibleChildrenCount</A>, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SwappingListBasicUI()"><!-- --></A><H3>
+SwappingListBasicUI</H3>
+<PRE>
+public <B>SwappingListBasicUI</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="createMouseInputListener()"><!-- --></A><H3>
+createMouseInputListener</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A> <B>createMouseInputListener</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#createMouseInputListener()">createMouseInputListener</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">BasicListUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="convertYToRow(int)"><!-- --></A><H3>
+convertYToRow</H3>
+<PRE>
+protected int <B>convertYToRow</B>(int y)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html#convertYToRow(int)">convertYToRow</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html">BasicListUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getJList()"><!-- --></A><H3>
+getJList</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JList.html">JList</A> <B>getJList</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SwappingListBasicUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.plaf.basic.BasicListUI">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-frame.html
new file mode 100644
index 0000000..525de26
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.misc()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.misc()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.misc</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ChunkyListModel.html" TARGET="classFrame">ChunkyListModel</A>
+<BR>
+<A HREF="SwappingListBasicUI.html" TARGET="classFrame">SwappingListBasicUI</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-summary.html
new file mode 100644
index 0000000..c1f4006
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-summary.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.misc()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.misc()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.misc
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ChunkyListModel.html">ChunkyListModel</A></B></TD>
+<TD>ChunkyListModel.java
+
+ This is a small extension to the list model class.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SwappingListBasicUI.html">SwappingListBasicUI</A></B></TD>
+<TD>SwappingListBasicUI.java
+
+ This class enables dragging of list items around something like
+ XMMS's playlist.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-tree.html
new file mode 100644
index 0000000..13c6be4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/misc/package-tree.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.misc Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.misc Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.misc
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/AbstractListModel.html"><B>AbstractListModel</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ListModel.html">ListModel</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.misc.<A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/ChunkyListModel.html"><B>ChunkyListModel</B></A></UL>
+<LI TYPE="circle">class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.MouseInputHandler.html"><B>BasicListUI.MouseInputHandler</B></A> (implements javax.swing.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.misc.<A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.SwappingMouseInputHandler.html"><B>SwappingListBasicUI.SwappingMouseInputHandler</B></A></UL>
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html"><B>ComponentUI</B></A><UL>
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ListUI.html"><B>ListUI</B></A><UL>
+<LI TYPE="circle">class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicListUI.html"><B>BasicListUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.misc.<A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.html"><B>SwappingListBasicUI</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html
new file mode 100644
index 0000000..6631d29
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html
@@ -0,0 +1,788 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:43 BST 2002 -->
+<TITLE>
+OptionableJFrame
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="OptionableJFrame";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableJFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.optionable</FONT>
+<BR>
+Class OptionableJFrame</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">java.awt.Window</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">java.awt.Frame</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">javax.swing.JFrame</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.optionable.OptionableJFrame</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>, <A HREF="http://java.sun.com/product [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.html">CinemaAlignmentFrame</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>OptionableJFrame</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></DL>
+
+<P>
+OptionableJFrame.java
+
+
+ Created: Fri May 07 16:45:36 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: OptionableJFrame.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.optionable.OptionableJFrame">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.AccessibleJFrame.html">JFrame.AccessibleJFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.AccessibleAWTFrame.html">Frame.AccessibleAWTFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.AccessibleAWTWindow.html">Window.AccessibleAWTWindow</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#EXIT_ON_CLOSE">EXIT_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPane">rootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPaneCheckingEnabled">rootPaneCheckingEnabled</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#CROSSHAIR_CURSOR">CROSSHAIR_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#DEFAULT_CURSOR">DEFAULT_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#E_RESIZE_CURSOR">E_RESIZE_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#HAND_CURSOR">HAND_CURSOR</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html">WindowConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DISPOSE_ON_CLOSE">DISPOSE_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DO_NOTHING_ON_CLOSE">DO_NOTHING_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#HIDE_ON_CLOSE">HIDE_ON_CLOSE</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String)">OptionableJFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, boolean)">OptionableJFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ boolean delayOptionable)</CODE>
+
+<BR>
+ No title.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, java.lang.String)">OptionableJFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ An internal frame with a title</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, java.lang.String, boolean)">OptionableJFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ boolean delayOptionable)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#OptionableJFrame(java.lang.String, java.lang.String, boolean, uk.ac.man.bioinf.apps.optionable.OptionHandler)">OptionableJFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ boolean delayOptionable,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> handler)</CODE>
+
+<BR>
+ A title and the ability to delay the registering of the optionable
+ status</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#defaultPack()">defaultPack</A></B>()</CODE>
+
+<BR>
+ Pack the frame if the size hasnt been sized by its options</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#forceOptionable()">forceOptionable</A></B>()</CODE>
+
+<BR>
+ Force the setting the optionable status now.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getDefaultOptionHandler()">getDefaultOptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptionGroupName()">getOptionGroupName</A></B>()</CODE>
+
+<BR>
+ Subclasses must provide this, either on a class or instance basis</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptionHandler()">getOptionHandler</A></B>()</CODE>
+
+<BR>
+ Implementation of the Optionable interface</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#getOptions()">getOptions</A></B>()</CODE>
+
+<BR>
+ An implementation of the Optionable interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultLocation(int, int)">setDefaultLocation</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ Pretty much the same as setDefaultSize</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setDefaultOptionHandler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultSize(int, int)">setDefaultSize</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ This sets the size of the frame, only if it hasnt been set as an option.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setOptionHandler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</CODE>
+
+<BR>
+ Implementation of the OptionableInterface</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptions()">setOptions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setOptions(java.lang.Object)">setOptions</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> param1)</CODE>
+
+<BR>
+ Implementation of the Optionable Interface.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#createRootPane()">createRootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#frameInit()">frameInit</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#getAccessibleContext()">getAccessib [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getCursorType()">getCursorType</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getExtendedState()">getExtendedState</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addWindowFocusListener(java.awt.event.WindowFocusL [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#getFont()">getFont</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#postEvent(java.awt.Event)">postEvent</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="OptionableJFrame(java.lang.String)"><!-- --></A><H3>
+OptionableJFrame</H3>
+<PRE>
+public <B>OptionableJFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="OptionableJFrame(java.lang.String, java.lang.String)"><!-- --></A><H3>
+OptionableJFrame</H3>
+<PRE>
+public <B>OptionableJFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+<DD>An internal frame with a title
+<P>
+<DT><B>Parameters:</B><DD><CODE>title</CODE> - </DL>
+<HR>
+
+<A NAME="OptionableJFrame(java.lang.String, boolean)"><!-- --></A><H3>
+OptionableJFrame</H3>
+<PRE>
+public <B>OptionableJFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ boolean delayOptionable)</PRE>
+<DL>
+<DD>No title. However if the param is true this class will not register
+ its optionable status until explicitly told, rather than in the constructor.
+ Subclasses which have their own options should use this option if they need
+ to complete their own setOptions before their constructor is complete.
+<P>
+<DT><B>Parameters:</B><DD><CODE>delayOptionable</CODE> - delay setting options until explicitly told<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#forceOptionable()"><CODE>forceOptionable()</CODE></A></DL>
+<HR>
+
+<A NAME="OptionableJFrame(java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>
+OptionableJFrame</H3>
+<PRE>
+public <B>OptionableJFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ boolean delayOptionable)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="OptionableJFrame(java.lang.String, java.lang.String, boolean, uk.ac.man.bioinf.apps.optionable.OptionHandler)"><!-- --></A><H3>
+OptionableJFrame</H3>
+<PRE>
+public <B>OptionableJFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ boolean delayOptionable,
+ <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> handler)</PRE>
+<DL>
+<DD>A title and the ability to delay the registering of the optionable
+ status
+<P>
+<DT><B>Parameters:</B><DD><CODE>optionableName</CODE> - the name used to identify this Frame to the
+ optionable library.<DD><CODE>title</CODE> - the title<DD><CODE>delayOptionable</CODE> - delay setting optionable status</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setOptions()"><!-- --></A><H3>
+setOptions</H3>
+<PRE>
+public void <B>setOptions</B>()
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">OptionableStateException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">OptionableStateException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="forceOptionable()"><!-- --></A><H3>
+forceOptionable</H3>
+<PRE>
+protected void <B>forceOptionable</B>()</PRE>
+<DL>
+<DD>Force the setting the optionable status now. This method
+ excepts if it is called more than once per object, or if a constructor without
+ the delayOptionable parameter has NOT been used
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></CODE> - if called illegally</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDefaultSize(int, int)"><!-- --></A><H3>
+setDefaultSize</H3>
+<PRE>
+public void <B>setDefaultSize</B>(int x,
+ int y)</PRE>
+<DL>
+<DD>This sets the size of the frame, only if it hasnt been set as an option. This
+ allows a default size to be set outside the constructor. The setSize() method
+ sets the size regardless of whether it has been set previously
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the width<DD><CODE>y</CODE> - the height</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDefaultLocation(int, int)"><!-- --></A><H3>
+setDefaultLocation</H3>
+<PRE>
+public void <B>setDefaultLocation</B>(int x,
+ int y)</PRE>
+<DL>
+<DD>Pretty much the same as setDefaultSize
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the x location<DD><CODE>y</CODE> - the y location<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html#setDefaultSize(int, int)"><CODE>setDefaultSize(int, int)</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="defaultPack()"><!-- --></A><H3>
+defaultPack</H3>
+<PRE>
+public void <B>defaultPack</B>()</PRE>
+<DL>
+<DD>Pack the frame if the size hasnt been sized by its options
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptions()"><!-- --></A><H3>
+getOptions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getOptions</B>()</PRE>
+<DL>
+<DD>An implementation of the Optionable interface. Subclasses overriding this method
+ should call super.getOptions. Also the constructor documentation and the delayOptionable
+ parameter should be considered.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptions()">getOptions</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the options</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptions(java.lang.Object)"><!-- --></A><H3>
+setOptions</H3>
+<PRE>
+public void <B>setOptions</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> param1)</PRE>
+<DL>
+<DD>Implementation of the Optionable Interface.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)">setOptions</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - <DT><B>See Also:</B><DD><CODE>getOptions</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><!-- --></A><H3>
+setOptionHandler</H3>
+<PRE>
+public void <B>setOptionHandler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</PRE>
+<DL>
+<DD>Implementation of the OptionableInterface
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setOptionHandler</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionHandler</CODE> - the value to assign to OptionHandler</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionHandler()"><!-- --></A><H3>
+getOptionHandler</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getOptionHandler</B>()</PRE>
+<DL>
+<DD>Implementation of the Optionable interface
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionHandler()">getOptionHandler</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the option handler</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionGroupName()"><!-- --></A><H3>
+getOptionGroupName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getOptionGroupName</B>()</PRE>
+<DL>
+<DD>Subclasses must provide this, either on a class or instance basis
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionGroupName()">getOptionGroupName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the Option group name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDefaultOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><!-- --></A><H3>
+setDefaultOptionHandler</H3>
+<PRE>
+public static void <B>setDefaultOptionHandler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDefaultOptionHandler()"><!-- --></A><H3>
+getDefaultOptionHandler</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getDefaultOptionHandler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableJFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html
new file mode 100644
index 0000000..4d5349f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html
@@ -0,0 +1,634 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:44 BST 2002 -->
+<TITLE>
+OptionableJSplitPane
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="OptionableJSplitPane";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableJSplitPane.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JSplitPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JSplitPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.optionable</FONT>
+<BR>
+Class OptionableJSplitPane</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">javax.swing.JSplitPane</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>, <A HREF="http://java.sun.com/product [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>OptionableJSplitPane</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">JSplitPane</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></DL>
+
+<P>
+OptionableJSplitPane.java
+
+ Stores the divider location as an option
+
+ Created: Fri Feb 2 17:55:18 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: OptionableJSplitPane.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JSplitPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">JSplitPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.AccessibleJSplitPane.html">JSplitPane.AccessibleJSplitPane</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JSplitPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">JSplitPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#CONTINUOUS_LAYOUT_PROPERTY">CONTINUOUS_LAYOUT_PROPERTY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#continuousLayout">continuousLayout</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#DIVIDER">DIVIDER</A>, <A HREF= [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#OptionableJSplitPane(java.lang.String)">OptionableJSplitPane</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#OptionableJSplitPane(java.lang.String, int)">OptionableJSplitPane</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ int orientation)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#forceOptionable()">forceOptionable</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getDefaultOptionHandler()">getDefaultOptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getOptionGroupName()">getOptionGroupName</A></B>()</CODE>
+
+<BR>
+ This string is used as an identifier for the groups
+ of options.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getOptionHandler()">getOptionHandler</A></B>()</CODE>
+
+<BR>
+ Get the value of OptionHandler.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#getOptions()">getOptions</A></B>()</CODE>
+
+<BR>
+ This method provides the current state of object as a map
+ of objects</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setDefaultDividerLocation(int)">setDefaultDividerLocation</A></B>(int location)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setDefaultOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setDefaultOptionHandler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setOptionHandler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</CODE>
+
+<BR>
+ Set the value of OptionHandler.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setOptions()">setOptions</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html#setOptions(java.lang.Object)">setOptions</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> options)</CODE>
+
+<BR>
+ Sets the options for this object</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JSplitPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html">JSplitPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html#getBottomComponent()">getBottomComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSpli [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="OptionableJSplitPane(java.lang.String)"><!-- --></A><H3>
+OptionableJSplitPane</H3>
+<PRE>
+public <B>OptionableJSplitPane</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="OptionableJSplitPane(java.lang.String, int)"><!-- --></A><H3>
+OptionableJSplitPane</H3>
+<PRE>
+public <B>OptionableJSplitPane</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> optionableName,
+ int orientation)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setDefaultDividerLocation(int)"><!-- --></A><H3>
+setDefaultDividerLocation</H3>
+<PRE>
+public void <B>setDefaultDividerLocation</B>(int location)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptions()"><!-- --></A><H3>
+setOptions</H3>
+<PRE>
+public void <B>setOptions</B>()
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">OptionableStateException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionableStateException.html">OptionableStateException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="forceOptionable()"><!-- --></A><H3>
+forceOptionable</H3>
+<PRE>
+protected void <B>forceOptionable</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptions()"><!-- --></A><H3>
+getOptions</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getOptions</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></B></DD>
+<DD>This method provides the current state of object as a map
+ of objects
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptions()">getOptions</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the options</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptions(java.lang.Object)"><!-- --></A><H3>
+setOptions</H3>
+<PRE>
+public void <B>setOptions</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> options)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></B></DD>
+<DD>Sets the options for this object
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptions(java.lang.Object)">setOptions</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><!-- --></A><H3>
+setOptionHandler</H3>
+<PRE>
+public void <B>setOptionHandler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></B></DD>
+<DD>Set the value of OptionHandler.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#setOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)">setOptionHandler</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>optionHandler</CODE> - the value to assign to OptionHandler</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionHandler()"><!-- --></A><H3>
+getOptionHandler</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getOptionHandler</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></B></DD>
+<DD>Get the value of OptionHandler.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionHandler()">getOptionHandler</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>Value of OptionHandler.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getOptionGroupName()"><!-- --></A><H3>
+getOptionGroupName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getOptionGroupName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></B></DD>
+<DD>This string is used as an identifier for the groups
+ of options. It will probably be used on a per-instance
+ basis, but could also be shared by all members of a class
+ or by an entire application. It should probably however
+ remain constant over time for any given Optionable object
+ If more than one optionable object is registered with
+ the same option handler and have the same group name the
+ options retrieved from one object will over ride all of the
+ others.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html#getOptionGroupName()">getOptionGroupName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the string by the group of options is known</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDefaultOptionHandler(uk.ac.man.bioinf.apps.optionable.OptionHandler)"><!-- --></A><H3>
+setDefaultOptionHandler</H3>
+<PRE>
+public static void <B>setDefaultOptionHandler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> optionHandler)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDefaultOptionHandler()"><!-- --></A><H3>
+getDefaultOptionHandler</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/OptionHandler.html">OptionHandler</A> <B>getDefaultOptionHandler</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="OptionableJSplitPane.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JSplitPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JSplitPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-frame.html
new file mode 100644
index 0000000..2429fa9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.optionable()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.optionable()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.optionable</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="OptionableJFrame.html" TARGET="classFrame">OptionableJFrame</A>
+<BR>
+<A HREF="OptionableJSplitPane.html" TARGET="classFrame">OptionableJSplitPane</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-summary.html
new file mode 100644
index 0000000..5380751
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-summary.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.optionable()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.optionable()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.optionable
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="OptionableJFrame.html">OptionableJFrame</A></B></TD>
+<TD>OptionableJFrame.java
+
+
+ Created: Fri May 07 16:45:36 1999</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="OptionableJSplitPane.html">OptionableJSplitPane</A></B></TD>
+<TD>OptionableJSplitPane.java
+
+ Stores the divider location as an option
+
+ Created: Fri Feb 2 17:55:18 2001</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-tree.html
new file mode 100644
index 0000000..47c1c04
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/optionable/package-tree.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.optionable Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.optionable Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.optionable
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSplitPane.html"><B>JSplitPane</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.html"><B>OptionableJSplitPane</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>)
+</UL>
+</UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/OptionableJFrame.html"><B>OptionableJFrame</B></A> (implements uk.ac.man.bioinf.apps.optionable.<A HREF="../../../../../../uk/ac/man/bioinf/apps/optionable/Optionable.html">Optionable</A>)
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/misc/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/ApplicationFrame.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/ApplicationFrame.html
new file mode 100644
index 0000000..42f9207
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/ApplicationFrame.html
@@ -0,0 +1,852 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:45 BST 2002 -->
+<TITLE>
+ApplicationFrame
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ApplicationFrame";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ApplicationFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util</FONT>
+<BR>
+Class ApplicationFrame</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">java.awt.Window</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">java.awt.Frame</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">javax.swing.JFrame</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.ApplicationFrame</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, <A HREF="http:/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ApplicationFrame</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></DL>
+
+<P>
+Provides a JFrame with a menu, a tool bar, a mainwindow and a status bar.
+ The class also provides access to resources.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>1.0</DD>
+</DD>
+<DT><B>Author:</B><DD>C.Miller</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.ApplicationFrame">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.AccessibleJFrame.html">JFrame.AccessibleJFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.AccessibleAWTFrame.html">Frame.AccessibleAWTFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.AccessibleAWTWindow.html">Window.AccessibleAWTWindow</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#EXIT_ON_CLOSE">EXIT_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPane">rootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPaneCheckingEnabled">rootPaneCheckingEnabled</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#CROSSHAIR_CURSOR">CROSSHAIR_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#DEFAULT_CURSOR">DEFAULT_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#E_RESIZE_CURSOR">E_RESIZE_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#HAND_CURSOR">HAND_CURSOR</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html">WindowConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DISPOSE_ON_CLOSE">DISPOSE_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DO_NOTHING_ON_CLOSE">DO_NOTHING_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#HIDE_ON_CLOSE">HIDE_ON_CLOSE</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#ApplicationFrame()">ApplicationFrame</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#ApplicationFrame(java.lang.String)">ApplicationFrame</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> resourceName)</CODE>
+
+<BR>
+ Create an Application frame with the resources specified.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addButton(java.lang.String)">addButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName)</CODE>
+
+<BR>
+ add a button with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addButton(java.lang.String, java.lang.String)">addButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName)</CODE>
+
+<BR>
+ add a button with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addButton(java.lang.String, java.lang.String, java.lang.String)">addButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> tooltipName)</CODE>
+
+<BR>
+ add a button with the specified text label, icon and tooltip.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenu.html">JMenu</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addMenu(java.lang.String)">addMenu</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> resourceName)</CODE>
+
+<BR>
+ add a menu with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addMenuItem(java.lang.String, java.lang.String)">addMenuItem</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName)</CODE>
+
+<BR>
+ create a menu with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenu.html">JMenu</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addSubMenu(java.lang.String, java.lang.String)">addSubMenu</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName)</CODE>
+
+<BR>
+ create a menu with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToggleButton.html">JToggleButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addToggleButton(java.lang.String)">addToggleButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName)</CODE>
+
+<BR>
+ add a button with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToggleButton.html">JToggleButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addToggleButton(java.lang.String, java.lang.String)">addToggleButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName)</CODE>
+
+<BR>
+ add a button with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToggleButton.html">JToggleButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#addToggleButton(java.lang.String, java.lang.String, java.lang.String)">addToggleButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> tooltipName)</CODE>
+
+<BR>
+ add a button with the specified text label, icon and tooltip.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#getContents()">getContents</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#getResourceAdapter()">getResourceAdapter</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#removeButton(java.lang.String)">removeButton</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName)</CODE>
+
+<BR>
+ remove a menu with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenu.html">JMenu</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#removeMenu(java.lang.String)">removeMenu</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> resourceName)</CODE>
+
+<BR>
+ remove a menu with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#removeMenuItem(java.lang.String)">removeMenuItem</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName)</CODE>
+
+<BR>
+ remove a menu item with the specified text label.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#setContents(javax.swing.JComponent)">setContents</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#setMenuEnabled(java.lang.String, boolean)">setMenuEnabled</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuName,
+ boolean enabled)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#setMenuItemEnabled(java.lang.String, boolean)">setMenuItemEnabled</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName,
+ boolean enabled)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#showInitialSplash()">showInitialSplash</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html#showMessage(java.lang.String)">showMessage</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#createRootPane()">createRootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#frameInit()">frameInit</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#getAccessibleContext()">getAccessib [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getCursorType()">getCursorType</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getExtendedState()">getExtendedState</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addWindowFocusListener(java.awt.event.WindowFocusL [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#getFont()">getFont</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#postEvent(java.awt.Event)">postEvent</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ApplicationFrame()"><!-- --></A><H3>
+ApplicationFrame</H3>
+<PRE>
+public <B>ApplicationFrame</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ApplicationFrame(java.lang.String)"><!-- --></A><H3>
+ApplicationFrame</H3>
+<PRE>
+public <B>ApplicationFrame</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> resourceName)</PRE>
+<DL>
+<DD>Create an Application frame with the resources specified.
+ <ul>
+ <li> will try to get a title for the frame from the property message.appName.title
+ <li> will try to get a URL to show in the initial content pane from helpURL.appName.initialSplash
+ <li> stops window closing with a dialog box - lables this using message.appName.quit and message.appName.quitTitle
+ </ul>
+<P>
+<DT><B>Parameters:</B><DD><CODE>resourceName</CODE> - looks in the package resources.locale.<resourceName> for a properties file</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addMenu(java.lang.String)"><!-- --></A><H3>
+addMenu</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenu.html">JMenu</A> <B>addMenu</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> resourceName)</PRE>
+<DL>
+<DD>add a menu with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>resourceName</CODE> - use the text specified in ApplicationFrame.Menu.<resource name></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeMenu(java.lang.String)"><!-- --></A><H3>
+removeMenu</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenu.html">JMenu</A> <B>removeMenu</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> resourceName)</PRE>
+<DL>
+<DD>remove a menu with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>resourceName</CODE> - use the text specified in ApplicationFrame.Menu.<resource name></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addMenuItem(java.lang.String, java.lang.String)"><!-- --></A><H3>
+addMenuItem</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>addMenuItem</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>create a menu with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>menuName</CODE> - add to the specified menu<DD><CODE>menuItemName</CODE> - use the text specified in ApplicationFrame.MenuItem.<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeMenuItem(java.lang.String)"><!-- --></A><H3>
+removeMenuItem</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenuItem.html">JMenuItem</A> <B>removeMenuItem</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>remove a menu item with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>menuItemName</CODE> - use the text specified in ApplicationFrame.MenuItem.<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSubMenu(java.lang.String, java.lang.String)"><!-- --></A><H3>
+addSubMenu</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JMenu.html">JMenu</A> <B>addSubMenu</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>create a menu with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>menuName</CODE> - add to the specified menu
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMenuEnabled(java.lang.String, boolean)"><!-- --></A><H3>
+setMenuEnabled</H3>
+<PRE>
+public void <B>setMenuEnabled</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuName,
+ boolean enabled)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMenuItemEnabled(java.lang.String, boolean)"><!-- --></A><H3>
+setMenuItemEnabled</H3>
+<PRE>
+public void <B>setMenuItemEnabled</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> menuItemName,
+ boolean enabled)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addButton(java.lang.String)"><!-- --></A><H3>
+addButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>addButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>add a button with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>labelName</CODE> - use the text specified in ApplicationFrame.Button.label<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addButton(java.lang.String, java.lang.String)"><!-- --></A><H3>
+addButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>addButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>add a button with the specified text label. and icon
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>labelName</CODE> - use the text specified in message.<app_name>.Button.label<resource name><DD><CODE>iconName</CODE> - use the image specified in image.<app_name>.Button.label<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addButton(java.lang.String, java.lang.String, java.lang.String)"><!-- --></A><H3>
+addButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>addButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> tooltipName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>add a button with the specified text label, icon and tooltip.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>labelName</CODE> - use the text specified in message.<app_name>.Button.label<resource name><DD><CODE>iconName</CODE> - use the image specified in image.<app_name>.Button.label<resource name><DD><CODE>tooltipName</CODE> - use the text specified in tooltip.<app_name>.Button.label<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addToggleButton(java.lang.String)"><!-- --></A><H3>
+addToggleButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToggleButton.html">JToggleButton</A> <B>addToggleButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>add a button with the specified text label.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>labelName</CODE> - use the text specified in ApplicationFrame.Button.label<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addToggleButton(java.lang.String, java.lang.String)"><!-- --></A><H3>
+addToggleButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToggleButton.html">JToggleButton</A> <B>addToggleButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>add a button with the specified text label. and icon
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>labelName</CODE> - use the text specified in message.<app_name>.Button.label<resource name><DD><CODE>iconName</CODE> - use the image specified in image.<app_name>.Button.label<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addToggleButton(java.lang.String, java.lang.String, java.lang.String)"><!-- --></A><H3>
+addToggleButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JToggleButton.html">JToggleButton</A> <B>addToggleButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> iconName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> tooltipName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>add a button with the specified text label, icon and tooltip.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>labelName</CODE> - use the text specified in message.<app_name>.Button.label<resource name><DD><CODE>iconName</CODE> - use the image specified in image.<app_name>.Button.label<resource name><DD><CODE>tooltipName</CODE> - use the text specified in tooltip.<app_name>.Button.label<resource name>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeButton(java.lang.String)"><!-- --></A><H3>
+removeButton</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> <B>removeButton</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> labelName)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></PRE>
+<DL>
+<DD>remove a menu with the specified text label.
+<P>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="showInitialSplash()"><!-- --></A><H3>
+showInitialSplash</H3>
+<PRE>
+public void <B>showInitialSplash</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getResourceAdapter()"><!-- --></A><H3>
+getResourceAdapter</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A> <B>getResourceAdapter</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setContents(javax.swing.JComponent)"><!-- --></A><H3>
+setContents</H3>
+<PRE>
+public void <B>setContents</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getContents()"><!-- --></A><H3>
+getContents</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>getContents</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="showMessage(java.lang.String)"><!-- --></A><H3>
+showMessage</H3>
+<PRE>
+public void <B>showMessage</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ApplicationFrame.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html
new file mode 100644
index 0000000..546c24c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html
@@ -0,0 +1,239 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:47 BST 2002 -->
+<TITLE>
+PopUpHtmlDisplay
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PopUpHtmlDisplay";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PopUpHtmlDisplay.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util</FONT>
+<BR>
+Class PopUpHtmlDisplay</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.PopUpHtmlDisplay</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>PopUpHtmlDisplay</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Displays an URL with a single 'OK' button at the bottom
+<P>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html#getPage(java.net.URL)">getPage</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> page)</CODE>
+
+<BR>
+ try to open the URL and get the page</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html#show(java.awt.Component, java.net.URL)">show</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> frame,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> page)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="show(java.awt.Component, java.net.URL)"><!-- --></A><H3>
+show</H3>
+<PRE>
+public static void <B>show</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> frame,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> page)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPage(java.net.URL)"><!-- --></A><H3>
+getPage</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>getPage</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> page)</PRE>
+<DL>
+<DD>try to open the URL and get the page
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PopUpHtmlDisplay.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/TripletPanel.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/TripletPanel.html
new file mode 100644
index 0000000..b6cd233
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/TripletPanel.html
@@ -0,0 +1,489 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:47 BST 2002 -->
+<TITLE>
+TripletPanel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="TripletPanel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="TripletPanel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util</FONT>
+<BR>
+Class TripletPanel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">javax.swing.JPanel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.TripletPanel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>TripletPanel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></DL>
+
+<P>
+Triplet panel provides a GUI Component with three sub components.
+ There is a main window on the right handsied and two sub windows on the left.
+ The relative sacing of these windows is controlled by split panes.
+ Methods exist to add and remove Components from these windows.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id :</DD>
+</DD>
+<DT><B>Author:</B><DD>C. Miller</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.TripletPanel">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.AccessibleJPanel.html">JPanel.AccessibleJPanel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#TripletPanel()">TripletPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#TripletPanel(javax.swing.JComponent, javax.swing.JComponent, javax.swing.JComponent)">TripletPanel</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> topLeft,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> bottomLeft,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> mainWindow)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#getBottomLeft()">getBottomLeft</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#getMainWindow()">getMainWindow</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#getTopLeft()">getTopLeft</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#setBottomLeft(javax.swing.JComponent)">setBottomLeft</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#setMainWindow(javax.swing.JComponent)">setMainWindow</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html#setTopLeft(javax.swing.JComponent)">setTopLeft</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUI()">getUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUIClassID()">getUIClassID</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#paramString()">paramString</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="TripletPanel()"><!-- --></A><H3>
+TripletPanel</H3>
+<PRE>
+public <B>TripletPanel</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="TripletPanel(javax.swing.JComponent, javax.swing.JComponent, javax.swing.JComponent)"><!-- --></A><H3>
+TripletPanel</H3>
+<PRE>
+public <B>TripletPanel</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> topLeft,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> bottomLeft,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> mainWindow)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setMainWindow(javax.swing.JComponent)"><!-- --></A><H3>
+setMainWindow</H3>
+<PRE>
+public void <B>setMainWindow</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMainWindow()"><!-- --></A><H3>
+getMainWindow</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>getMainWindow</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setTopLeft(javax.swing.JComponent)"><!-- --></A><H3>
+setTopLeft</H3>
+<PRE>
+public void <B>setTopLeft</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTopLeft()"><!-- --></A><H3>
+getTopLeft</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>getTopLeft</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setBottomLeft(javax.swing.JComponent)"><!-- --></A><H3>
+setBottomLeft</H3>
+<PRE>
+public void <B>setBottomLeft</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getBottomLeft()"><!-- --></A><H3>
+getBottomLeft</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>getBottomLeft</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="TripletPanel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/DecimalField.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/DecimalField.html
new file mode 100644
index 0000000..51df24f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/DecimalField.html
@@ -0,0 +1,481 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:48 BST 2002 -->
+<TITLE>
+DecimalField
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DecimalField";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DecimalField.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JTextField">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JTextField">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class DecimalField</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">javax.swing.text.JTextComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">javax.swing.JTextField</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.DecimalField</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Scrollable.html">Scrollable</A>, <A HREF="http://java.sun.com/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DecimalField</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></DL>
+
+<P>
+Provides a validated field that only accepts decimal numbers.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>1.0</DD>
+</DD>
+<DT><B>Author:</B><DD>C.Miller</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.DecimalField">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.AccessibleJTextField.html">JTextField.AccessibleJTextField</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.AccessibleJTextComponent.html">JTextComponent.AccessibleJTextComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.KeyBinding.html">JTextComponent.KeyBinding</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#notifyAction">notifyAction</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#DEFAULT_KEYMAP">DEFAULT_KEYMAP</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#FOCUS_ACCELERATOR_KEY">FOCUS_ACCELERATOR_KEY</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.SwingConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#CENTER">CENTER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#EAST">EAST</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#HORIZONTAL">HORIZONTAL</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html#DecimalField(double, int, java.text.NumberFormat)">DecimalField</A></B>(double value,
+ int columns,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> f)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html#DecimalField(int, java.text.NumberFormat)">DecimalField</A></B>(int columns,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> f)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> double</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html#getValue()">getValue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html#isValid()">isValid</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html#setValue(double)">setValue</A></B>(double value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#addActionListener(java.awt.event.ActionListener)">addActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#configurePropertiesFromAction(javax.swing.Action)">configurePropertiesFromAction</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#createActionPropertyChangeListener(javax.swing.Action)">createActionProper [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addCaretListener(javax.swing.event.CaretListener)">addCaretListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addInputMethodListener(java.awt.event.InputMethodListener)">addInputMethodListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addKeymap(java.lang.String, javax.swing.text. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DecimalField(int, java.text.NumberFormat)"><!-- --></A><H3>
+DecimalField</H3>
+<PRE>
+public <B>DecimalField</B>(int columns,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> f)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DecimalField(double, int, java.text.NumberFormat)"><!-- --></A><H3>
+DecimalField</H3>
+<PRE>
+public <B>DecimalField</B>(double value,
+ int columns,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/NumberFormat.html">NumberFormat</A> f)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isValid()"><!-- --></A><H3>
+isValid</H3>
+<PRE>
+public boolean <B>isValid</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#isValid()">isValid</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getValue()"><!-- --></A><H3>
+getValue</H3>
+<PRE>
+public double <B>getValue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setValue(double)"><!-- --></A><H3>
+setValue</H3>
+<PRE>
+public void <B>setValue</B>(double value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DecimalField.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JTextField">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JTextField">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html
new file mode 100644
index 0000000..c50ddb3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html
@@ -0,0 +1,370 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:49 BST 2002 -->
+<TITLE>
+FormattedDocument
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FormattedDocument";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FormattedDocument.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.text.AbstractDocument">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.text.PlainDocument">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class FormattedDocument</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">javax.swing.text.AbstractDocument</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">javax.swing.text.PlainDocument</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.FormattedDocument</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FormattedDocument</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></DL>
+
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.FormattedDocument">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.AbstractElement.html">AbstractDocument.AbstractElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.AttributeContext.html">AbstractDocument.AttributeContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.BranchElement.html">AbstractDocument.BranchElement</A>, <A HREF="http://java.sun.com/products [...]
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.PlainDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#lineLimitAttribute">lineLimitAttribute</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#tabSizeAttribute">tabSizeAttribute</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#BAD_LOCATION">BAD_LOCATION</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#BidiElementName">BidiElementName</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#ContentElementName">ContentElementName</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocume [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.Document"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html#StreamDescriptionProperty">StreamDescriptionProperty</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html#TitleProperty">TitleProperty</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#FormattedDocument(java.text.Format)">FormattedDocument</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/Format.html">Format</A> f)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/Format.html">Format</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#getFormat()">getFormat</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)">insertString</A></B>(int offs,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> str,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AttributeSet.html">AttributeSet</A> a)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html#remove(int, int)">remove</A></B>(int offs,
+ int len)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.PlainDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#createDefaultRoot()">createDefaultRoot</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#getDefaultRootElement()">getDefaultRootElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#getParagraphElement(int)">getParagraphElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/s [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#addDocumentListener(javax.swing.event.DocumentListener)">addDocumentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#addUndoableEditListener(javax.swing.event.UndoableEditListener)">addUndoableEditListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#createBranchElement(java [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FormattedDocument(java.text.Format)"><!-- --></A><H3>
+FormattedDocument</H3>
+<PRE>
+public <B>FormattedDocument</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/Format.html">Format</A> f)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFormat()"><!-- --></A><H3>
+getFormat</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/text/Format.html">Format</A> <B>getFormat</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertString(int, java.lang.String, javax.swing.text.AttributeSet)"><!-- --></A><H3>
+insertString</H3>
+<PRE>
+public void <B>insertString</B>(int offs,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> str,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AttributeSet.html">AttributeSet</A> a)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>insertString</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)">insertString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocumen [...]
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(int, int)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public void <B>remove</B>(int offs,
+ int len)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>remove</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#remove(int, int)">remove</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FormattedDocument.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.text.AbstractDocument">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.text.PlainDocument">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html
new file mode 100644
index 0000000..5dc6f53
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:50 BST 2002 -->
+<TITLE>
+IntegerField.IntegerDocument
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="IntegerField.IntegerDocument";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntegerField.IntegerDocument.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.text.AbstractDocument">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.text.PlainDocument">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class IntegerField.IntegerDocument</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">javax.swing.text.AbstractDocument</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">javax.swing.text.PlainDocument</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html">IntegerField</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>protected class <B>IntegerField.IntegerDocument</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></DL>
+
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.IntegerField.IntegerDocument">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.AbstractElement.html">AbstractDocument.AbstractElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.AttributeContext.html">AbstractDocument.AttributeContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.BranchElement.html">AbstractDocument.BranchElement</A>, <A HREF="http://java.sun.com/products [...]
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.PlainDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#lineLimitAttribute">lineLimitAttribute</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#tabSizeAttribute">tabSizeAttribute</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#BAD_LOCATION">BAD_LOCATION</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#BidiElementName">BidiElementName</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#ContentElementName">ContentElementName</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocume [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.Document"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html#StreamDescriptionProperty">StreamDescriptionProperty</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html#TitleProperty">TitleProperty</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html#IntegerField.IntegerDocument()">IntegerField.IntegerDocument</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)">insertString</A></B>(int offs,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> str,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AttributeSet.html">AttributeSet</A> a)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.PlainDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#createDefaultRoot()">createDefaultRoot</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#getDefaultRootElement()">getDefaultRootElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#getParagraphElement(int)">getParagraphElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/s [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#addDocumentListener(javax.swing.event.DocumentListener)">addDocumentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#addUndoableEditListener(javax.swing.event.UndoableEditListener)">addUndoableEditListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#createBranchElement(java [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IntegerField.IntegerDocument()"><!-- --></A><H3>
+IntegerField.IntegerDocument</H3>
+<PRE>
+protected <B>IntegerField.IntegerDocument</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="insertString(int, java.lang.String, javax.swing.text.AttributeSet)"><!-- --></A><H3>
+insertString</H3>
+<PRE>
+public void <B>insertString</B>(int offs,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> str,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AttributeSet.html">AttributeSet</A> a)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>insertString</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)">insertString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocumen [...]
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntegerField.IntegerDocument.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.text.AbstractDocument">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.text.PlainDocument">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/IntegerField.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/IntegerField.html
new file mode 100644
index 0000000..084464b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/IntegerField.html
@@ -0,0 +1,499 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:49 BST 2002 -->
+<TITLE>
+IntegerField
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="IntegerField";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntegerField.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JTextField">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class IntegerField</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">javax.swing.text.JTextComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">javax.swing.JTextField</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.IntegerField</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Scrollable.html">Scrollable</A>, <A HREF="http://java.sun.com/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>IntegerField</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></DL>
+
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.IntegerField">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html">IntegerField.IntegerDocument</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.AccessibleJTextField.html">JTextField.AccessibleJTextField</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.AccessibleJTextComponent.html">JTextComponent.AccessibleJTextComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.KeyBinding.html">JTextComponent.KeyBinding</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#notifyAction">notifyAction</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#DEFAULT_KEYMAP">DEFAULT_KEYMAP</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#FOCUS_ACCELERATOR_KEY">FOCUS_ACCELERATOR_KEY</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.SwingConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#CENTER">CENTER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#EAST">EAST</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#HORIZONTAL">HORIZONTAL</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html#IntegerField(int)">IntegerField</A></B>(int columns)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html#IntegerField(int, int)">IntegerField</A></B>(int value,
+ int columns)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html#createDefaultModel()">createDefaultModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html#getValue()">getValue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html#isValid()">isValid</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html#setValue(int)">setValue</A></B>(int value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#addActionListener(java.awt.event.ActionListener)">addActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#configurePropertiesFromAction(javax.swing.Action)">configurePropertiesFromAction</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#createActionPropertyChangeListener(javax.swing.Action)">createActionProper [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addCaretListener(javax.swing.event.CaretListener)">addCaretListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addInputMethodListener(java.awt.event.InputMethodListener)">addInputMethodListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addKeymap(java.lang.String, javax.swing.text. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IntegerField(int)"><!-- --></A><H3>
+IntegerField</H3>
+<PRE>
+public <B>IntegerField</B>(int columns)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="IntegerField(int, int)"><!-- --></A><H3>
+IntegerField</H3>
+<PRE>
+public <B>IntegerField</B>(int value,
+ int columns)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isValid()"><!-- --></A><H3>
+isValid</H3>
+<PRE>
+public boolean <B>isValid</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#isValid()">isValid</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getValue()"><!-- --></A><H3>
+getValue</H3>
+<PRE>
+public int <B>getValue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setValue(int)"><!-- --></A><H3>
+setValue</H3>
+<PRE>
+public void <B>setValue</B>(int value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createDefaultModel()"><!-- --></A><H3>
+createDefaultModel</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A> <B>createDefaultModel</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#createDefaultModel()">createDefaultModel</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntegerField.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JTextField">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html
new file mode 100644
index 0000000..dcb9057
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html
@@ -0,0 +1,533 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:50 BST 2002 -->
+<TITLE>
+PasswordDialog
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PasswordDialog";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PasswordDialog.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class PasswordDialog</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.PasswordDialog</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>PasswordDialog</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Pop up Dialog box to get a password off a user.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>1.0</DD>
+</DD>
+<DT><B>Author:</B><DD>C.Miller</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#parent">parent</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPasswordField.html">JPasswordField</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#password">password</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JCheckBox.html">JCheckBox</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#remember">remember</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#userName">userName</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame)">PasswordDialog</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String)">PasswordDialog</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> userNameLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> passwordLabel)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String, java.lang.String, java.lang.String)">PasswordDialog</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> userNameLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> passwordLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialUserName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialPassword)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean)">PasswordDialog</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> userNameLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> passwordLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> rememberLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialUserName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialPassword,
+ boolean initialRemember)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#getPassword()">getPassword</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#getPasswordPane()">getPasswordPane</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#getUserName()">getUserName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#isPasswordToBeRemembered()">isPasswordToBeRemembered</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#setPassword(java.lang.String)">setPassword</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> pw)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#setRememberPassword(boolean)">setRememberPassword</A></B>(boolean r)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#setUserName(java.lang.String)">setUserName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> un)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html#show()">show</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="parent"><!-- --></A><H3>
+parent</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> <B>parent</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="userName"><!-- --></A><H3>
+userName</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A> <B>userName</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="password"><!-- --></A><H3>
+password</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPasswordField.html">JPasswordField</A> <B>password</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="remember"><!-- --></A><H3>
+remember</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JCheckBox.html">JCheckBox</A> <B>remember</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PasswordDialog(javax.swing.JFrame)"><!-- --></A><H3>
+PasswordDialog</H3>
+<PRE>
+public <B>PasswordDialog</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String)"><!-- --></A><H3>
+PasswordDialog</H3>
+<PRE>
+public <B>PasswordDialog</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> userNameLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> passwordLabel)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String, java.lang.String, java.lang.String)"><!-- --></A><H3>
+PasswordDialog</H3>
+<PRE>
+public <B>PasswordDialog</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> userNameLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> passwordLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialUserName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialPassword)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="PasswordDialog(javax.swing.JFrame, java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>
+PasswordDialog</H3>
+<PRE>
+public <B>PasswordDialog</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A> parent,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> userNameLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> passwordLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> rememberLabel,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialUserName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> initialPassword,
+ boolean initialRemember)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="show()"><!-- --></A><H3>
+show</H3>
+<PRE>
+public void <B>show</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPassword()"><!-- --></A><H3>
+getPassword</H3>
+<PRE>
+public char[] <B>getPassword</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUserName()"><!-- --></A><H3>
+getUserName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getUserName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setPassword(java.lang.String)"><!-- --></A><H3>
+setPassword</H3>
+<PRE>
+public void <B>setPassword</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> pw)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setUserName(java.lang.String)"><!-- --></A><H3>
+setUserName</H3>
+<PRE>
+public void <B>setUserName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> un)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isPasswordToBeRemembered()"><!-- --></A><H3>
+isPasswordToBeRemembered</H3>
+<PRE>
+public boolean <B>isPasswordToBeRemembered</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setRememberPassword(boolean)"><!-- --></A><H3>
+setRememberPassword</H3>
+<PRE>
+public void <B>setRememberPassword</B>(boolean r)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPasswordPane()"><!-- --></A><H3>
+getPasswordPane</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> <B>getPasswordPane</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PasswordDialog.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html
new file mode 100644
index 0000000..48be781
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html
@@ -0,0 +1,776 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:50 BST 2002 -->
+<TITLE>
+ValidatedForm
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ValidatedForm";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ValidatedForm.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class ValidatedForm</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">javax.swing.JPanel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.ValidatedForm</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ValidatedForm</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></DL>
+
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.ValidatedForm">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.AccessibleJPanel.html">JPanel.AccessibleJPanel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#EQUALS">EQUALS</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#GREATER_THAN">GREATER_THAN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#LESS_THAN">LESS_THAN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#LIKE">LIKE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#ValidatedForm()">ValidatedForm</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addDecimalField(java.lang.String, java.lang.String, boolean, int, boolean)">addDecimalField</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ boolean modifier,
+ int columns,
+ boolean isPercent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addDecimalField(java.lang.String, java.lang.String, double, boolean, int, boolean)">addDecimalField</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ double init,
+ boolean modifier,
+ int columns,
+ boolean isPercent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addIntegerField(java.lang.String, java.lang.String, boolean, int)">addIntegerField</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ boolean modifier,
+ int columns)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addIntegerField(java.lang.String, java.lang.String, int, boolean, int)">addIntegerField</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ int init,
+ boolean modifier,
+ int columns)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#addTextField(java.lang.String, java.lang.String, java.lang.String, boolean, int)">addTextField</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> init,
+ boolean modifier,
+ int columns)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> double</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getDecimalFieldValue(java.lang.String)">getDecimalFieldValue</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getIntegerFieldValue(java.lang.String)">getIntegerFieldValue</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getModifierType(java.lang.String)">getModifierType</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#getTextFieldValue(java.lang.String)">getTextFieldValue</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#isDecimalFieldValid(java.lang.String)">isDecimalFieldValid</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#isIntegerFieldValid(java.lang.String)">isIntegerFieldValid</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#isTextFieldValid(java.lang.String)">isTextFieldValid</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setDecimalFieldValue(java.lang.String, double)">setDecimalFieldValue</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ double v)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setIntegerFieldValue(java.lang.String, int)">setIntegerFieldValue</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ int v)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setModifierType(java.lang.String, int)">setModifierType</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ int t)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html#setTextFieldValue(java.lang.String, java.lang.String)">setTextFieldValue</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> v)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUI()">getUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUIClassID()">getUIClassID</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#paramString()">paramString</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="LESS_THAN"><!-- --></A><H3>
+LESS_THAN</H3>
+<PRE>
+public static final int <B>LESS_THAN</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.util.forms.ValidatedForm.LESS_THAN">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="GREATER_THAN"><!-- --></A><H3>
+GREATER_THAN</H3>
+<PRE>
+public static final int <B>GREATER_THAN</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.util.forms.ValidatedForm.GREATER_THAN">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="EQUALS"><!-- --></A><H3>
+EQUALS</H3>
+<PRE>
+public static final int <B>EQUALS</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.util.forms.ValidatedForm.EQUALS">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="LIKE"><!-- --></A><H3>
+LIKE</H3>
+<PRE>
+public static final int <B>LIKE</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.util.forms.ValidatedForm.LIKE">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ValidatedForm()"><!-- --></A><H3>
+ValidatedForm</H3>
+<PRE>
+public <B>ValidatedForm</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addIntegerField(java.lang.String, java.lang.String, int, boolean, int)"><!-- --></A><H3>
+addIntegerField</H3>
+<PRE>
+public void <B>addIntegerField</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ int init,
+ boolean modifier,
+ int columns)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIntegerField(java.lang.String, java.lang.String, boolean, int)"><!-- --></A><H3>
+addIntegerField</H3>
+<PRE>
+public void <B>addIntegerField</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ boolean modifier,
+ int columns)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addDecimalField(java.lang.String, java.lang.String, double, boolean, int, boolean)"><!-- --></A><H3>
+addDecimalField</H3>
+<PRE>
+public void <B>addDecimalField</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ double init,
+ boolean modifier,
+ int columns,
+ boolean isPercent)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addDecimalField(java.lang.String, java.lang.String, boolean, int, boolean)"><!-- --></A><H3>
+addDecimalField</H3>
+<PRE>
+public void <B>addDecimalField</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ boolean modifier,
+ int columns,
+ boolean isPercent)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addTextField(java.lang.String, java.lang.String, java.lang.String, boolean, int)"><!-- --></A><H3>
+addTextField</H3>
+<PRE>
+public void <B>addTextField</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> label,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> init,
+ boolean modifier,
+ int columns)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIntegerFieldValue(java.lang.String)"><!-- --></A><H3>
+getIntegerFieldValue</H3>
+<PRE>
+public int <B>getIntegerFieldValue</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDecimalFieldValue(java.lang.String)"><!-- --></A><H3>
+getDecimalFieldValue</H3>
+<PRE>
+public double <B>getDecimalFieldValue</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTextFieldValue(java.lang.String)"><!-- --></A><H3>
+getTextFieldValue</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTextFieldValue</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isIntegerFieldValid(java.lang.String)"><!-- --></A><H3>
+isIntegerFieldValid</H3>
+<PRE>
+public boolean <B>isIntegerFieldValid</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isDecimalFieldValid(java.lang.String)"><!-- --></A><H3>
+isDecimalFieldValid</H3>
+<PRE>
+public boolean <B>isDecimalFieldValid</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isTextFieldValid(java.lang.String)"><!-- --></A><H3>
+isTextFieldValid</H3>
+<PRE>
+public boolean <B>isTextFieldValid</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setIntegerFieldValue(java.lang.String, int)"><!-- --></A><H3>
+setIntegerFieldValue</H3>
+<PRE>
+public void <B>setIntegerFieldValue</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ int v)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setDecimalFieldValue(java.lang.String, double)"><!-- --></A><H3>
+setDecimalFieldValue</H3>
+<PRE>
+public void <B>setDecimalFieldValue</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ double v)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setTextFieldValue(java.lang.String, java.lang.String)"><!-- --></A><H3>
+setTextFieldValue</H3>
+<PRE>
+public void <B>setTextFieldValue</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> v)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModifierType(java.lang.String)"><!-- --></A><H3>
+getModifierType</H3>
+<PRE>
+public int <B>getModifierType</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setModifierType(java.lang.String, int)"><!-- --></A><H3>
+setModifierType</H3>
+<PRE>
+public void <B>setModifierType</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> key,
+ int t)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ValidatedForm.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html
new file mode 100644
index 0000000..7badc3b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:55 BST 2002 -->
+<TITLE>
+WholeNumberField.WholeNumberDocument
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="WholeNumberField.WholeNumberDocument";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WholeNumberField.WholeNumberDocument.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.text.AbstractDocument">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.text.PlainDocument">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class WholeNumberField.WholeNumberDocument</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">javax.swing.text.AbstractDocument</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">javax.swing.text.PlainDocument</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html">WholeNumberField</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>protected class <B>WholeNumberField.WholeNumberDocument</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></DL>
+
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.WholeNumberField.WholeNumberDocument">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.AbstractElement.html">AbstractDocument.AbstractElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.AttributeContext.html">AbstractDocument.AttributeContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.BranchElement.html">AbstractDocument.BranchElement</A>, <A HREF="http://java.sun.com/products [...]
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.PlainDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#lineLimitAttribute">lineLimitAttribute</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#tabSizeAttribute">tabSizeAttribute</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#BAD_LOCATION">BAD_LOCATION</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#BidiElementName">BidiElementName</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#ContentElementName">ContentElementName</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocume [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.Document"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html#StreamDescriptionProperty">StreamDescriptionProperty</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html#TitleProperty">TitleProperty</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html#WholeNumberField.WholeNumberDocument()">WholeNumberField.WholeNumberDocument</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)">insertString</A></B>(int offs,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> str,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AttributeSet.html">AttributeSet</A> a)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.PlainDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html">PlainDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#createDefaultRoot()">createDefaultRoot</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#getDefaultRootElement()">getDefaultRootElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#getParagraphElement(int)">getParagraphElement</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/s [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.AbstractDocument"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html">AbstractDocument</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#addDocumentListener(javax.swing.event.DocumentListener)">addDocumentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#addUndoableEditListener(javax.swing.event.UndoableEditListener)">addUndoableEditListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html#createBranchElement(java [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="WholeNumberField.WholeNumberDocument()"><!-- --></A><H3>
+WholeNumberField.WholeNumberDocument</H3>
+<PRE>
+protected <B>WholeNumberField.WholeNumberDocument</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="insertString(int, java.lang.String, javax.swing.text.AttributeSet)"><!-- --></A><H3>
+insertString</H3>
+<PRE>
+public void <B>insertString</B>(int offs,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> str,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AttributeSet.html">AttributeSet</A> a)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>insertString</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html#insertString(int, java.lang.String, javax.swing.text.AttributeSet)">insertString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocumen [...]
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/BadLocationException.html">BadLocationException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WholeNumberField.WholeNumberDocument.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.text.AbstractDocument">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.text.PlainDocument">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html
new file mode 100644
index 0000000..2fedb57
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html
@@ -0,0 +1,467 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:54 BST 2002 -->
+<TITLE>
+WholeNumberField
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="WholeNumberField";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WholeNumberField.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JTextField">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.util.forms</FONT>
+<BR>
+Class WholeNumberField</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">javax.swing.text.JTextComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">javax.swing.JTextField</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.util.forms.WholeNumberField</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Scrollable.html">Scrollable</A>, <A HREF="http://java.sun.com/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>WholeNumberField</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></DL>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: WholeNumberField.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>C.Miller</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.util.forms.WholeNumberField">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html">WholeNumberField.WholeNumberDocument</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.AccessibleJTextField.html">JTextField.AccessibleJTextField</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.AccessibleJTextComponent.html">JTextComponent.AccessibleJTextComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.KeyBinding.html">JTextComponent.KeyBinding</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#notifyAction">notifyAction</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#DEFAULT_KEYMAP">DEFAULT_KEYMAP</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#FOCUS_ACCELERATOR_KEY">FOCUS_ACCELERATOR_KEY</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.SwingConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#CENTER">CENTER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#EAST">EAST</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#HORIZONTAL">HORIZONTAL</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#WholeNumberField(int, int)">WholeNumberField</A></B>(int value,
+ int columns)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#createDefaultModel()">createDefaultModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#getValue()">getValue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html#setValue(int)">setValue</A></B>(int value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JTextField"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#addActionListener(java.awt.event.ActionListener)">addActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#configurePropertiesFromAction(javax.swing.Action)">configurePropertiesFromAction</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#createActionPropertyChangeListener(javax.swing.Action)">createActionProper [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.text.JTextComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html">JTextComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addCaretListener(javax.swing.event.CaretListener)">addCaretListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addInputMethodListener(java.awt.event.InputMethodListener)">addInputMethodListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html#addKeymap(java.lang.String, javax.swing.text. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="WholeNumberField(int, int)"><!-- --></A><H3>
+WholeNumberField</H3>
+<PRE>
+public <B>WholeNumberField</B>(int value,
+ int columns)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getValue()"><!-- --></A><H3>
+getValue</H3>
+<PRE>
+public int <B>getValue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setValue(int)"><!-- --></A><H3>
+setValue</H3>
+<PRE>
+public void <B>setValue</B>(int value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createDefaultModel()"><!-- --></A><H3>
+createDefaultModel</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A> <B>createDefaultModel</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html#createDefaultModel()">createDefaultModel</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html">JTextField</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.WholeNumberDocument.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WholeNumberField.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JTextField">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-frame.html
new file mode 100644
index 0000000..c0eda92
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-frame.html
@@ -0,0 +1,42 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.util.forms()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.util.forms()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.util.forms</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="DecimalField.html" TARGET="classFrame">DecimalField</A>
+<BR>
+<A HREF="FormattedDocument.html" TARGET="classFrame">FormattedDocument</A>
+<BR>
+<A HREF="IntegerField.html" TARGET="classFrame">IntegerField</A>
+<BR>
+<A HREF="PasswordDialog.html" TARGET="classFrame">PasswordDialog</A>
+<BR>
+<A HREF="ValidatedForm.html" TARGET="classFrame">ValidatedForm</A>
+<BR>
+<A HREF="WholeNumberField.html" TARGET="classFrame">WholeNumberField</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-summary.html
new file mode 100644
index 0000000..550a5f7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-summary.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.util.forms()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.util.forms()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.util.forms
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DecimalField.html">DecimalField</A></B></TD>
+<TD>Provides a validated field that only accepts decimal numbers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FormattedDocument.html">FormattedDocument</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="IntegerField.html">IntegerField</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PasswordDialog.html">PasswordDialog</A></B></TD>
+<TD>Pop up Dialog box to get a password off a user.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ValidatedForm.html">ValidatedForm</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="WholeNumberField.html">WholeNumberField</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-tree.html
new file mode 100644
index 0000000..8f62f72
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/forms/package-tree.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.util.forms Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.util.forms Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.util.forms
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/AbstractDocument.html"><B>AbstractDocument</B></A> (implements javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/Document.html">Document</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/PlainDocument.html"><B>PlainDocument</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/FormattedDocument.html"><B>FormattedDocument</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.IntegerDocument.html"><B>IntegerField.IntegerDocument</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberF [...]
+</UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html"><B>JPanel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/ValidatedForm.html"><B>ValidatedForm</B></A></UL>
+<LI TYPE="circle">class javax.swing.text.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/text/JTextComponent.html"><B>JTextComponent</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Scrollable.html">Scrollable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JTextField.html"><B>JTextField</B></A> (implements javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/DecimalField.html"><B>DecimalField</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/IntegerField.html"><B>IntegerField</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/WholeNumberField.html"><B>WholeNumberField</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.forms.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/forms/PasswordDialog.html"><B>PasswordDialog</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/util/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/package-frame.html
new file mode 100644
index 0000000..c20479a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/package-frame.html
@@ -0,0 +1,36 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.util()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.util()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/gui/util/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.util</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ApplicationFrame.html" TARGET="classFrame">ApplicationFrame</A>
+<BR>
+<A HREF="PopUpHtmlDisplay.html" TARGET="classFrame">PopUpHtmlDisplay</A>
+<BR>
+<A HREF="TripletPanel.html" TARGET="classFrame">TripletPanel</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/package-summary.html
new file mode 100644
index 0000000..67b4683
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/package-summary.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.util()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.util()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.util
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ApplicationFrame.html">ApplicationFrame</A></B></TD>
+<TD>Provides a JFrame with a menu, a tool bar, a mainwindow and a status bar.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PopUpHtmlDisplay.html">PopUpHtmlDisplay</A></B></TD>
+<TD>Displays an URL with a single 'OK' button at the bottom</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="TripletPanel.html">TripletPanel</A></B></TD>
+<TD>Triplet panel provides a GUI Component with three sub components.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/util/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/util/package-tree.html
new file mode 100644
index 0000000..41c9a41
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/util/package-tree.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.util Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.util Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.util
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html"><B>JPanel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.<A HREF="../../../../../../uk/ac/man/bioinf/gui/util/TripletPanel.html"><B>TripletPanel</B></A></UL>
+</UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.<A HREF="../../../../../../uk/ac/man/bioinf/gui/util/ApplicationFrame.html"><B>ApplicationFrame</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.util.<A HREF="../../../../../../uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.html"><B>PopUpHtmlDisplay</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/optionable/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html
new file mode 100644
index 0000000..dbfeaa1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html
@@ -0,0 +1,469 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:55 BST 2002 -->
+<TITLE>
+AlignmentSelectionModel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentSelectionModel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Interface AlignmentSelectionModel</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentSelectionModel</B></DL>
+
+<P>
+AlignmentSelectionModel.java
+
+ This defines the selection model for the JAlignmentViewer. The main
+ three methods of this class, namely stopSelection(),
+ extendSelection() and clearSelection() are called by the
+ JAlignmentViewer, or one of its helper classes and usually
+ considered to be advisory. The model is free to ignore these method
+ calls if it is appropriate behaviour.
+
+ Created: Mon Apr 10 11:32:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentSelectionModel.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#clearSelection()">clearSelection</A></B>()</CODE>
+
+<BR>
+ Clear all the selections in this model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Start a selection at the given point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></B>()</CODE>
+
+<BR>
+ Returns the current selection or null if there is no
+ selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></B>()</CODE>
+
+<BR>
+ Get the number of selections.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get the first selection rectangle which surrounds the point, or
+ null if there is not one.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get all selection rectangles which surround this point, or null
+ if there is not one</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></B>(int index)</CODE>
+
+<BR>
+ Gets the given selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Is the point within one of the selection rectangles</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isSelecting()">isSelecting</A></B>()</CODE>
+
+<BR>
+ is the current selection in the process of being selected.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Complete the selection at the given point</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isSelecting()"><!-- --></A><H3>
+isSelecting</H3>
+<PRE>
+public boolean <B>isSelecting</B>()</PRE>
+<DL>
+<DD>is the current selection in the process of being selected.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>true is selection is changing</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentSelection()"><!-- --></A><H3>
+getCurrentSelection</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getCurrentSelection</B>()</PRE>
+<DL>
+<DD>Returns the current selection or null if there is no
+ selection. If there is more than one selection this should return
+ the most recently made selection
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSelections()"><!-- --></A><H3>
+getNumberSelections</H3>
+<PRE>
+public int <B>getNumberSelections</B>()</PRE>
+<DL>
+<DD>Get the number of selections.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of selections</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionAt(int)"><!-- --></A><H3>
+getSelectionAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSelectionAt</B>(int index)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IndexOutOfBoundsException.html">IndexOutOfBoundsException</A></PRE>
+<DL>
+<DD>Gets the given selection. The index should reflect the
+ chronological order in which the selections were made, with the
+ smallest index first
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index
+<DT><B>Returns:</B><DD>the selection array index at the given index
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ArrayIndexOutOfBoundsException.html">ArrayIndexOutOfBoundsException</A></CODE> - if the index is out of bounds
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IndexOutOfBoundsException.html">IndexOutOfBoundsException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+isPointSelected</H3>
+<PRE>
+public boolean <B>isPointSelected</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Is the point within one of the selection rectangles
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point
+<DT><B>Returns:</B><DD>true if point is within a rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection()"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>()</PRE>
+<DL>
+<DD>Clear all the selections in this model
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectangleAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getRectangleAtPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Get the first selection rectangle which surrounds the point, or
+ null if there is not one.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangle surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectanglesAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[] <B>getRectanglesAtPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Get all selection rectangles which surround this point, or null
+ if there is not one
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangles surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+extendSelection</H3>
+<PRE>
+public void <B>extendSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Start a selection at the given point
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the start of the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+stopSelection</H3>
+<PRE>
+public void <B>stopSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Complete the selection at the given point
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point to complete the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+addAlignmentSelectionListener</H3>
+<PRE>
+public void <B>addAlignmentSelectionListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+removeAlignmentSelectionListener</H3>
+<PRE>
+public void <B>removeAlignmentSelectionListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html
new file mode 100644
index 0000000..9c75c8f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html
@@ -0,0 +1,226 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:56 BST 2002 -->
+<TITLE>
+AlignmentSelectionRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentSelectionRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Interface AlignmentSelectionRenderer</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html">DefaultAlignmentSelectionRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentSelectionRenderer</B></DL>
+
+<P>
+SelectionRenderer.java
+
+
+ Created: Wed Mar 7 18:45:50 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentSelectionRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html#renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">renderAlignmentSelection</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+renderAlignmentSelection</H3>
+<PRE>
+public void <B>renderAlignmentSelection</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..de4c59c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html
@@ -0,0 +1,237 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:56 BST 2002 -->
+<TITLE>
+AlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Interface AlignmentViewerCellRenderer</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html">DefaultAlignmentViewerCellRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentViewerCellRenderer</B></DL>
+
+<P>
+AlignmentViewerCellRenderer.java
+
+ Initial interface for the AlignmentViewerCellRender. This defines a
+ component which is used to render an individual cell for a
+ JAlignmentViewer. Its not complete yet. Its needs information about
+ the colour model to be used for this cell. And possible info about
+ the difference between the alignment position, and the viewer
+ position, Im not sure.
+
+ Created: Mon Mar 20 15:50:14 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentViewerCellRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html#getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">getAlignmentViewerCellRendererComponent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoints)</CODE>
+
+<BR>
+ This method should be able to cope with null values for element
+ which will be passed if we are off the front or the end of the sequence</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+getAlignmentViewerCellRendererComponent</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> <B>getAlignmentViewerCellRendererComponent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoints)</PRE>
+<DL>
+<DD>This method should be able to cope with null values for element
+ which will be passed if we are off the front or the end of the sequence
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>viewer</CODE> - <DD><CODE>element</CODE> - <DD><CODE>bgColor</CODE> - the background color of the cell (can be null)<DD><CODE>isSelected</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..cfa3a57
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:57 BST 2002 -->
+<TITLE>
+BorderFastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BorderFastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BorderFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class BorderFastAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.BorderFastAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BorderFastAlignmentViewerCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DL>
+
+<P>
+BorderFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer. This one deals specifically with the border to
+ the cell.
+ <p>
+ By default, it will probably be drawn second (after the color), but
+ all of this is determined by the RendererManager.
+
+ Created: Fri Aug 25 14:06:17 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: BorderFastAlignmentViewerCellRenderer.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html#BorderFastAlignmentViewerCellRenderer()">BorderFastAlignmentViewerCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BorderFastAlignmentViewerCellRenderer()"><!-- --></A><H3>
+BorderFastAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>BorderFastAlignmentViewerCellRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignm [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>color</CODE> - the [...]
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BorderFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html
new file mode 100644
index 0000000..e752568
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html
@@ -0,0 +1,404 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:57 BST 2002 -->
+<TITLE>
+ButtonViewerPopupMenu
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ButtonViewerPopupMenu";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ButtonViewerPopupMenu.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPopupMenu">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class ButtonViewerPopupMenu</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html">javax.swing.JPopupMenu</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A>, <A HREF="http://java. [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ButtonViewerPopupMenu</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html">JPopupMenu</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A></DL>
+
+<P>
+ButtonViewerPopupMenu.java
+
+ This class implements a pop up menu for the
+ JAlignmentButtonPanel. The top menu item gives the title. This
+ serves as both a "tooltip" and a place to put buttons.
+
+ Created: Tue Oct 17 13:48:53 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ButtonViewerPopupMenu.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JPopupMenu"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html">JPopupMenu</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.AccessibleJPopupMenu.html">JPopupMenu.AccessibleJPopupMenu</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.Separator.html">JPopupMenu.Separator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html#ButtonViewerPopupMenu(uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel)">ButtonViewerPopupMenu</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A> panel)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html#getSelectedSequence()">getSelectedSequence</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html#itemStateChanged(java.awt.event.ItemEvent)">itemStateChanged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemEvent.html">ItemEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JPopupMenu"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html">JPopupMenu</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html#add(javax.swing.Action)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html#add(javax.swing.JMenuItem)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html#add(java.lang.String)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html#addPopupMenuListener(javax.swing.event.PopupMen [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ButtonViewerPopupMenu(uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel)"><!-- --></A><H3>
+ButtonViewerPopupMenu</H3>
+<PRE>
+public <B>ButtonViewerPopupMenu</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html">JAlignmentButtonPanel</A> panel)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSelectedSequence()"><!-- --></A><H3>
+getSelectedSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSelectedSequence</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="itemStateChanged(java.awt.event.ItemEvent)"><!-- --></A><H3>
+itemStateChanged</H3>
+<PRE>
+public void <B>itemStateChanged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemEvent.html">ItemEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>itemStateChanged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ButtonViewerPopupMenu.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPopupMenu">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..0043773
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:58 BST 2002 -->
+<TITLE>
+ColorFastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ColorFastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class ColorFastAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.ColorFastAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ColorFastAlignmentViewerCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DL>
+
+<P>
+ColorFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer. This one deals specifically with the color of the
+ cell (background).
+ <p>
+ By default, this will drawn first and other things placed on top of
+ it. However, all this will be determined by the RendererManager.
+
+ Created: Fri Aug 25 14:40:58 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ColorFastAlignmentViewerCellRenderer.java,v 1.5 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html#ColorFastAlignmentViewerCellRenderer()">ColorFastAlignmentViewerCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ColorFastAlignmentViewerCellRenderer()"><!-- --></A><H3>
+ColorFastAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>ColorFastAlignmentViewerCellRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignm [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>color</CODE> - the [...]
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ColorFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..0bea050
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html
@@ -0,0 +1,298 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:58 BST 2002 -->
+<TITLE>
+CursorLessFastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CursorLessFastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CursorLessFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class CursorLessFastAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.CursorLessFastAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CursorLessFastAlignmentViewerCellRenderer</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A></DL>
+
+<P>
+CursorLessFastAlignmentViewerCellRenderer.java
+
+
+ Created: Thu Jul 13 17:59:36 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CursorLessFastAlignmentViewerCellRenderer.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html#CursorLessFastAlignmentViewerCellRenderer(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">CursorLessFastAlignmentViewerCellRenderer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#calculateViableRenderers(int)">calculateViableRenderers</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CursorLessFastAlignmentViewerCellRenderer(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+CursorLessFastAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>CursorLessFastAlignmentViewerCellRenderer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignm [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>bgColor</CODE> - t [...]
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CursorLessFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html
new file mode 100644
index 0000000..40868a6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:59 BST 2002 -->
+<TITLE>
+DefaultAlignmentSelectionRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultAlignmentSelectionRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultAlignmentSelectionRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class DefaultAlignmentSelectionRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.DefaultAlignmentSelectionRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultAlignmentSelectionRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A></DL>
+
+<P>
+DefaultAlignmentSelectionRenderer.java
+
+
+ Created: Wed Mar 7 18:59:56 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultAlignmentSelectionRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html#DefaultAlignmentSelectionRenderer()">DefaultAlignmentSelectionRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html#renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">renderAlignmentSelection</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultAlignmentSelectionRenderer()"><!-- --></A><H3>
+DefaultAlignmentSelectionRenderer</H3>
+<PRE>
+public <B>DefaultAlignmentSelectionRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+renderAlignmentSelection</H3>
+<PRE>
+public void <B>renderAlignmentSelection</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html#renderAlignmentSelection(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">renderAlignmentSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultAlignmentSelectionRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..22b8045
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html
@@ -0,0 +1,415 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:59 BST 2002 -->
+<TITLE>
+DefaultAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JLabel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JLabel">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class DefaultAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">javax.swing.JLabel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultAlignmentViewerCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A></DL>
+
+<P>
+DefaultAlignmentViewerCellRenderer.java
+
+
+ Created: Mon Mar 20 20:23:12 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultAlignmentViewerCellRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.DefaultAlignmentViewerCellRenderer">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JLabel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.AccessibleJLabel.html">JLabel.AccessibleJLabel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JLabel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#labelFor">labelFor</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.SwingConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#CENTER">CENTER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#EAST">EAST</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#HORIZONTAL">HORIZONTAL</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html#DefaultAlignmentViewerCellRenderer()">DefaultAlignmentViewerCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html#getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">getAlignmentViewerCellRendererComponent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean cellHasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method should be able to cope with null values for element
+ which will be passed if we are off the front or the end of the sequence</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JLabel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html">JLabel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#checkHorizontalKey(int, java.lang.String)">checkHorizontalKey</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#checkVerticalKey(int, java.lang.String)">checkVerticalKey</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swin [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultAlignmentViewerCellRenderer()"><!-- --></A><H3>
+DefaultAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>DefaultAlignmentViewerCellRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+getAlignmentViewerCellRendererComponent</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> <B>getAlignmentViewerCellRendererComponent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean cellHasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method should be able to cope with null values for element
+ which will be passed if we are off the front or the end of the sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html#getAlignmentViewerCellRendererComponent(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">getAlignmentViewerCellRendererComponent</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRender [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>viewer</CODE> - <DD><CODE>element</CODE> - <DD><CODE>bgColor</CODE> - the background color of the cell (can be null)<DD><CODE>isSelected</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JLabel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JLabel">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..e2b459b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html
@@ -0,0 +1,318 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:59 BST 2002 -->
+<TITLE>
+DefaultFastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultFastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class DefaultFastAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.DefaultFastAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultFastAlignmentViewerCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DL>
+
+<P>
+DefaultFastAlignmentViewerCellRenderer.java
+
+
+ Created: Mon Apr 17 20:11:46 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultFastAlignmentViewerCellRenderer.java,v 1.6 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html#charArray">charArray</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html#DefaultFastAlignmentViewerCellRenderer()">DefaultFastAlignmentViewerCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="charArray"><!-- --></A><H3>
+charArray</H3>
+<PRE>
+public char[] <B>charArray</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultFastAlignmentViewerCellRenderer()"><!-- --></A><H3>
+DefaultFastAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>DefaultFastAlignmentViewerCellRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignm [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>bgColor</CODE> - t [...]
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html
new file mode 100644
index 0000000..467e9ee
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html
@@ -0,0 +1,388 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:59 BST 2002 -->
+<TITLE>
+DefaultSequenceCursor
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultSequenceCursor";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultSequenceCursor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class DefaultSequenceCursor</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.DefaultSequenceCursor</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultSequenceCursor</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></DL>
+
+<P>
+DefaultSequenceCursor.java
+
+
+ Created: Tue Apr 4 12:49:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultSequenceCursor.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#DefaultSequenceCursor()">DefaultSequenceCursor</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#addChangeListener(javax.swing.event.ChangeListener)">addChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ Add a listener to this cursor</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#getMark()">getMark</A></B>()</CODE>
+
+<BR>
+ Returns the position of mark</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#getPoint()">getPoint</A></B>()</CODE>
+
+<BR>
+ Returns the position of point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#removeChangeListener(javax.swing.event.ChangeListener)">removeChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ Remove the listener from this cursor</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#setMark()">setMark</A></B>()</CODE>
+
+<BR>
+ Set the mark to the current position of point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">setPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> position)</CODE>
+
+<BR>
+ Set the point to the new position</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultSequenceCursor()"><!-- --></A><H3>
+DefaultSequenceCursor</H3>
+<PRE>
+public <B>DefaultSequenceCursor</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+addChangeListener</H3>
+<PRE>
+public void <B>addChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></B></DD>
+<DD>Add a listener to this cursor
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#addChangeListener(javax.swing.event.ChangeListener)">addChangeListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to add</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+removeChangeListener</H3>
+<PRE>
+public void <B>removeChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></B></DD>
+<DD>Remove the listener from this cursor
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#removeChangeListener(javax.swing.event.ChangeListener)">removeChangeListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to remove</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+setPoint</H3>
+<PRE>
+public void <B>setPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> position)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></B></DD>
+<DD>Set the point to the new position
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">setPoint</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>position</CODE> - the position to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMark()"><!-- --></A><H3>
+setMark</H3>
+<PRE>
+public void <B>setMark</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></B></DD>
+<DD>Set the mark to the current position of point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#setMark()">setMark</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPoint()"><!-- --></A><H3>
+getPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getPoint</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></B></DD>
+<DD>Returns the position of point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#getPoint()">getPoint</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the position</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMark()"><!-- --></A><H3>
+getMark</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getMark</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></B></DD>
+<DD>Returns the position of mark
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#getMark()">getMark</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the position</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultSequenceCursor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..fc880ba
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html
@@ -0,0 +1,255 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:56 BST 2002 -->
+<TITLE>
+FastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Interface FastAlignmentViewerCellRenderer</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html">BorderFastAlignmentViewerCellRenderer</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html">ColorFastAlignmentViewerCellRenderer</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html">DefaultFastAlignmentViewerCellRenderer</A>, <A HREF="../../../. [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>FastAlignmentViewerCellRenderer</B></DL>
+
+<P>
+FastAlignmentViewerCellRenderer.java
+
+ Although the JAlignmentViewer provides a pluggable renderer
+ architecture with the AlignmentViewerCellRenderer it has been found
+ that this has a fairly disasterous effect on performance of the
+ viewer particularly with respect to scrolling, due to the large
+ number of method calls and events to render a cell. This class
+ circumvents all of that, and still provides a degree of
+ plugability. The disadvantage of using this class is that its much
+ lower level. You have to do all of the drawing directly onto the
+ Graphics context provided, and you can not just simply extend a JComponent.
+
+ This interface is the same as for the AlignmentViewerCellRenderer
+ with the additional information that is required, which is the
+ graphics context, where to draw on it, and the size to draw.
+
+ Created: Mon Apr 17 20:03:52 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FastAlignmentViewerCellRenderer.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>bgColor</CODE> - t [...]
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/Install.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/Install.html
new file mode 100644
index 0000000..95d5326
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/Install.html
@@ -0,0 +1,289 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:00 BST 2002 -->
+<TITLE>
+Install
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Install";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Install.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class Install</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.Install</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>Install</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DL>
+
+<P>
+Install.java
+
+ This class provides the install information for the all of the
+ classes in the viewer package. It is needed because a Swing
+ component discovers its UIDelegate by a run time class lookup. The
+ standard Swing classes get this information from the UIManager
+ which in turn gets them from the LookAndFeel classes. Since we cant
+ over ride these this is managed here. At the moment the different
+ look and feels are not supported (which is to stay that the look
+ and feel remains the same always!). To get this class to work, just
+ load it, by calling Install.class.
+
+ Created: Wed Mar 15 17:03:43 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Install.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html#Install()">Install</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html#installBasicLookAndFeel()">installBasicLookAndFeel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Install()"><!-- --></A><H3>
+Install</H3>
+<PRE>
+public <B>Install</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="installBasicLookAndFeel()"><!-- --></A><H3>
+installBasicLookAndFeel</H3>
+<PRE>
+public void <B>installBasicLookAndFeel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Install.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html
new file mode 100644
index 0000000..7c9afe2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html
@@ -0,0 +1,310 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:00 BST 2002 -->
+<TITLE>
+InvertedScrollPaneLayout
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvertedScrollPaneLayout";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvertedScrollPaneLayout.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.ScrollPaneLayout">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.ScrollPaneLayout">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class InvertedScrollPaneLayout</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">javax.swing.ScrollPaneLayout</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/LayoutManager.html">LayoutManager</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>InvertedScrollPaneLayout</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A></DL>
+
+<P>
+InvertedScrollPaneLayout.java
+
+
+ Created: Fri Mar 31 14:27:41 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InvertedScrollPaneLayout.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.ScrollPaneLayout"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.UIResource.html">ScrollPaneLayout.UIResource</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.ScrollPaneLayout"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#colHead">colHead</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#hsb">hsb</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#hsbPolicy">hsbPolicy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#lowerLeft">lowerLeft</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.ScrollPaneConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#COLUMN_HEADER">COLUMN_HEADER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#HORIZONTAL_SCROLLBAR">HORIZONTAL_SCROLLBAR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#HORIZONTAL_SCROLLBAR_ALWAYS">HORIZONTAL_SCROLLBAR_ALWAYS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/s [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html#InvertedScrollPaneLayout()">InvertedScrollPaneLayout</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html#layoutContainer(java.awt.Container)">layoutContainer</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A> parent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.ScrollPaneLayout"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#addLayoutComponent(java.lang.String, java.awt.Component)">addLayoutComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#addSingletonComponent(java.awt.Component, java.awt.Component)">addSingletonComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#getColumnHeader()">getColumnHeader</A>, <A [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvertedScrollPaneLayout()"><!-- --></A><H3>
+InvertedScrollPaneLayout</H3>
+<PRE>
+public <B>InvertedScrollPaneLayout</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="layoutContainer(java.awt.Container)"><!-- --></A><H3>
+layoutContainer</H3>
+<PRE>
+public void <B>layoutContainer</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A> parent)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>layoutContainer</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/LayoutManager.html">LayoutManager</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html#layoutContainer(java.awt.Container)">layoutContainer</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvertedScrollPaneLayout.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.ScrollPaneLayout">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.ScrollPaneLayout">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html
new file mode 100644
index 0000000..1626e4c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html
@@ -0,0 +1,692 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:01 BST 2002 -->
+<TITLE>
+JAlignmentButtonPanel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="JAlignmentButtonPanel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JAlignmentButtonPanel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class JAlignmentButtonPanel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">javax.swing.JPanel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="htt [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>JAlignmentButtonPanel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/ItemSelectable.html">ItemSelectable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></DL>
+
+<P>
+JAlignmentButtonPanel.java
+
+ This component provides a rank of Buttons relating to a
+ SequenceAlignment. At the moment it only supports Vertical
+ alignment. The labels of the buttons are what ever is specified by
+ the individual Sequence resourceString. These labels define the
+ width of the overall panel, whilst the height is defined by the
+ specified height of the individual cells.
+
+ Created: Fri May 19 16:24:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: JAlignmentButtonPanel.java,v 1.8 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.AccessibleJPanel.html">JPanel.AccessibleJPanel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#JAlignmentButtonPanel()">JAlignmentButtonPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#JAlignmentButtonPanel(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">JAlignmentButtonPanel</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#addItemListener(java.awt.event.ItemListener)">addItemListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#clearAllSequenceColors()">clearAllSequenceColors</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#clearSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">clearSequenceColor</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getPointForSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getPointForSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getPreferredSize()">getPreferredSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getSelectedObjects()">getSelectedObjects</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#getSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceColor</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#processItemEvent(java.awt.event.ItemEvent)">processItemEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemEvent.html">ItemEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#removeItemListener(java.awt.event.ItemListener)">removeItemListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setButton(uk.ac.man.bioinf.sequence.alignment.GappedSequence, javax.swing.JButton)">setButton</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> button)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setFixedCellHeight(int)">setFixedCellHeight</A></B>(int height)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html#setSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)">setSequenceColor</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUI()">getUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUIClassID()">getUIClassID</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#paramString()">paramString</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="JAlignmentButtonPanel()"><!-- --></A><H3>
+JAlignmentButtonPanel</H3>
+<PRE>
+public <B>JAlignmentButtonPanel</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JAlignmentButtonPanel(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+JAlignmentButtonPanel</H3>
+<PRE>
+public <B>JAlignmentButtonPanel</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setFixedCellHeight(int)"><!-- --></A><H3>
+setFixedCellHeight</H3>
+<PRE>
+public void <B>setFixedCellHeight</B>(int height)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPreferredSize()"><!-- --></A><H3>
+getPreferredSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getPreferredSize</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getPreferredSize()">getPreferredSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPointForSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getPointForSequence</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> <B>getPointForSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence, java.awt.Color)"><!-- --></A><H3>
+setSequenceColor</H3>
+<PRE>
+public void <B>setSequenceColor</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getSequenceColor</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> <B>getSequenceColor</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSequenceColor(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+clearSequenceColor</H3>
+<PRE>
+public void <B>clearSequenceColor</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearAllSequenceColors()"><!-- --></A><H3>
+clearAllSequenceColors</H3>
+<PRE>
+public void <B>clearAllSequenceColors</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setSequenceAlignment</H3>
+<PRE>
+public void <B>setSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setButton(uk.ac.man.bioinf.sequence.alignment.GappedSequence, javax.swing.JButton)"><!-- --></A><H3>
+setButton</H3>
+<PRE>
+public void <B>setButton</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JButton.html">JButton</A> button)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addItemListener(java.awt.event.ItemListener)"><!-- --></A><H3>
+addItemListener</H3>
+<PRE>
+public void <B>addItemListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>addItemListener</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/ItemSelectable.html">ItemSelectable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeItemListener(java.awt.event.ItemListener)"><!-- --></A><H3>
+removeItemListener</H3>
+<PRE>
+public void <B>removeItemListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>removeItemListener</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/ItemSelectable.html">ItemSelectable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectedObjects()"><!-- --></A><H3>
+getSelectedObjects</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] <B>getSelectedObjects</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>getSelectedObjects</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/ItemSelectable.html">ItemSelectable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="processItemEvent(java.awt.event.ItemEvent)"><!-- --></A><H3>
+processItemEvent</H3>
+<PRE>
+protected void <B>processItemEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemEvent.html">ItemEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JAlignmentButtonPanel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html
new file mode 100644
index 0000000..95a2008
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html
@@ -0,0 +1,671 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:03 BST 2002 -->
+<TITLE>
+JAlignmentRuler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="JAlignmentRuler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JAlignmentRuler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JSlider">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class JAlignmentRuler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">javax.swing.JSlider</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.JAlignmentRuler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>, <A HREF="http://java.sun.com/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>JAlignmentRuler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></DL>
+
+<P>
+JAlignmentRuler.java
+
+
+
+ Created: Thu Mar 23 12:33:50 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: JAlignmentRuler.java,v 1.6 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.JAlignmentRuler">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JSlider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.AccessibleJSlider.html">JSlider.AccessibleJSlider</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#preferredHeight">preferredHeight</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#uiClassID">uiClassID</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JSlider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#changeEvent">changeEvent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#changeListener">changeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#majorTickSpacing">majorTickSpacing</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#minorTickSpacing">minorTickSpacing</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.SwingConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#BOTTOM">BOTTOM</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#CENTER">CENTER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#EAST">EAST</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html#HORIZONTAL">HORIZONTAL</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler()">JAlignmentRuler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">JAlignmentRuler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)">JAlignmentRuler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq,
+ int orientation)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int, int)">JAlignmentRuler</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq,
+ int orientation,
+ int widthPerBase)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getMaximumSize()">getMaximumSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getMinimumSize()">getMinimumSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getPreferredHeight()">getPreferredHeight</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getPreferredWidthPerBase()">getPreferredWidthPerBase</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getSequenceAlignment()">getSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#getUIClassID()">getUIClassID</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#setPreferredWidthPerBase(int)">setPreferredWidthPerBase</A></B>(int widthPerBase)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#setUI(javax.swing.plaf.SliderUI)">setUI</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/SliderUI.html">SliderUI</A> ui)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html#updateUI()">updateUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JSlider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#addChangeListener(javax.swing.event.ChangeListener)">addChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#createChangeListener()">createChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#createStandardLabels(int)">createStandardLabels</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/sw [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="uiClassID"><!-- --></A><H3>
+uiClassID</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>uiClassID</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.gui.viewer.JAlignmentRuler.uiClassID">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="preferredHeight"><!-- --></A><H3>
+preferredHeight</H3>
+<PRE>
+protected int <B>preferredHeight</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="JAlignmentRuler()"><!-- --></A><H3>
+JAlignmentRuler</H3>
+<PRE>
+public <B>JAlignmentRuler</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+JAlignmentRuler</H3>
+<PRE>
+public <B>JAlignmentRuler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)"><!-- --></A><H3>
+JAlignmentRuler</H3>
+<PRE>
+public <B>JAlignmentRuler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq,
+ int orientation)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JAlignmentRuler(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int, int)"><!-- --></A><H3>
+JAlignmentRuler</H3>
+<PRE>
+public <B>JAlignmentRuler</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> seq,
+ int orientation,
+ int widthPerBase)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setSequenceAlignment</H3>
+<PRE>
+public void <B>setSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAlignment()"><!-- --></A><H3>
+getSequenceAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSequenceAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMinimumSize()"><!-- --></A><H3>
+getMinimumSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getMinimumSize</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getMinimumSize()">getMinimumSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMaximumSize()"><!-- --></A><H3>
+getMaximumSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getMaximumSize</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getMaximumSize()">getMaximumSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPreferredHeight()"><!-- --></A><H3>
+getPreferredHeight</H3>
+<PRE>
+public int <B>getPreferredHeight</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPreferredWidthPerBase()"><!-- --></A><H3>
+getPreferredWidthPerBase</H3>
+<PRE>
+public int <B>getPreferredWidthPerBase</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setPreferredWidthPerBase(int)"><!-- --></A><H3>
+setPreferredWidthPerBase</H3>
+<PRE>
+public void <B>setPreferredWidthPerBase</B>(int widthPerBase)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUIClassID()"><!-- --></A><H3>
+getUIClassID</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getUIClassID</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#getUIClassID()">getUIClassID</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setUI(javax.swing.plaf.SliderUI)"><!-- --></A><H3>
+setUI</H3>
+<PRE>
+public void <B>setUI</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/SliderUI.html">SliderUI</A> ui)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#setUI(javax.swing.plaf.SliderUI)">setUI</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="updateUI()"><!-- --></A><H3>
+updateUI</H3>
+<PRE>
+public void <B>updateUI</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html#updateUI()">updateUI</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html">JSlider</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JAlignmentRuler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JSlider">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html
new file mode 100644
index 0000000..d77bffb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html
@@ -0,0 +1,2037 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:05 BST 2002 -->
+<TITLE>
+JAlignmentViewer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="JAlignmentViewer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JAlignmentViewer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JComponent">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class JAlignmentViewer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.JAlignmentViewer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>JAlignmentViewer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSele [...]
+
+<P>
+JAlignmentViewer.java
+
+
+ Created: Tue Mar 14 16:28:59 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: JAlignmentViewer.java,v 1.28 2002/03/08 14:53:57 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.JAlignmentViewer">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#readonly">readonly</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#uiClassID">uiClassID</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#JAlignmentViewer()">JAlignmentViewer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#JAlignmentViewer(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">JAlignmentViewer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#addCursorChangeListener(javax.swing.event.ChangeListener)">addCursorChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#clearSelection()">clearSelection</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#deleteGapsAt(int, int, int)">deleteGapsAt</A></B>(int x,
+ int y,
+ int sizeOfGap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#deleteGapsAt(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int)">deleteGapsAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ int sizeOfGap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#deleteGapsAtCursor(int)">deleteGapsAtCursor</A></B>(int sizeOfGap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#ensureSequencePointIsVisible(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">ensureSequencePointIsVisible</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getAlignmentSelectionRenderer()">getAlignmentSelectionRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getCellBounds</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellHeight()">getCellHeight</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellRenderer()">getCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCellWidth()">getCellWidth</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getColorMap()">getColorMap</A></B>()</CODE>
+
+<BR>
+ Returns the current color map.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getCursorModel()">getCursorModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getFastCellRenderer()">getFastCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getMark()">getMark</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getMaximumSize()">getMaximumSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getMinimumSize()">getMinimumSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPoint()">getPoint</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPointAtSequencePoint(int, int)">getPointAtSequencePoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPreferredScrollableViewportSize()">getPreferredScrollableViewportSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getPreferredSize()">getPreferredSize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getRectangleForSequenceRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getRectangleForSequenceRectangle</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> seqRect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableBlockIncrement(java.awt.Rectangle, int, int)">getScrollableBlockIncrement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> visibleRect,
+ int orientation,
+ int direction)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableTracksViewportHeight()">getScrollableTracksViewportHeight</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableTracksViewportWidth()">getScrollableTracksViewportWidth</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getScrollableUnitIncrement(java.awt.Rectangle, int, int)">getScrollableUnitIncrement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> visibleRect,
+ int orientation,
+ int direction)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSelectionModel()">getSelectionModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSequenceAlignment()">getSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSequencePointAtPoint(int, int)">getSequencePointAtPoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getSequencePointAtPoint(java.awt.Point)">getSequencePointAtPoint</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getUIClassID()">getUIClassID</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#getVisibleSequenceRectangle()">getVisibleSequenceRectangle</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#insertGapsAt(int, int, int)">insertGapsAt</A></B>(int x,
+ int y,
+ int sizeOfGap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#insertGapsAt(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int)">insertGapsAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ int sizeOfGap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#insertGapsAtCursor(int)">insertGapsAtCursor</A></B>(int sizeOfGap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#isReadonly()">isReadonly</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursor(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">moveCursor</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> newPoint)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorBeginningOfAlignment()">moveCursorBeginningOfAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorBeginningOfSequence()">moveCursorBeginningOfSequence</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorDown(int)">moveCursorDown</A></B>(int number)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorEndOfAlignment()">moveCursorEndOfAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorEndOfSequence()">moveCursorEndOfSequence</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorLeft(int)">moveCursorLeft</A></B>(int number)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageDown()">moveCursorPageDown</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageLeft()">moveCursorPageLeft</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageRight()">moveCursorPageRight</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorPageUp()">moveCursorPageUp</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorRight(int)">moveCursorRight</A></B>(int number)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorToSequencePoint(int, int)">moveCursorToSequencePoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorToSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">moveCursorToSequencePoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#moveCursorUp(int)">moveCursorUp</A></B>(int number)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#removeCursorChangeListener(javax.swing.event.ChangeListener)">removeCursorChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setAlignmentSelectionRenderer(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer)">setAlignmentSelectionRenderer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A> selectionRenderer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCellHeight(int)">setCellHeight</A></B>(int height)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCellRenderer(uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer)">setCellRenderer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A> renderer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCellWidth(int)">setCellWidth</A></B>(int width)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)">setColorMap</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> colorMap)</CODE>
+
+<BR>
+ Changes the color map and notifies of change.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setCursorModel(uk.ac.man.bioinf.gui.viewer.SequenceCursor)">setCursorModel</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A> cursor)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setFastCellRenderer(uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)">setFastCellRenderer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A> renderer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setMark()">setMark</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">setPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setReadonly(boolean)">setReadonly</A></B>(boolean readonly)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)">setSelectionModel</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> selectionModel)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#setUI(uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI)">setUI</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A> ui)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#updateUI()">updateUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="uiClassID"><!-- --></A><H3>
+uiClassID</H3>
+<PRE>
+public static final <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>uiClassID</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../constant-values.html#uk.ac.man.bioinf.gui.viewer.JAlignmentViewer.uiClassID">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="readonly"><!-- --></A><H3>
+readonly</H3>
+<PRE>
+protected boolean <B>readonly</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="JAlignmentViewer()"><!-- --></A><H3>
+JAlignmentViewer</H3>
+<PRE>
+public <B>JAlignmentViewer</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JAlignmentViewer(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+JAlignmentViewer</H3>
+<PRE>
+public <B>JAlignmentViewer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setCellRenderer(uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer)"><!-- --></A><H3>
+setCellRenderer</H3>
+<PRE>
+public void <B>setCellRenderer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A> renderer)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellRenderer()"><!-- --></A><H3>
+getCellRenderer</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A> <B>getCellRenderer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setFastCellRenderer(uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer)"><!-- --></A><H3>
+setFastCellRenderer</H3>
+<PRE>
+public void <B>setFastCellRenderer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A> renderer)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFastCellRenderer()"><!-- --></A><H3>
+getFastCellRenderer</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A> <B>getFastCellRenderer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setAlignmentSelectionRenderer(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer)"><!-- --></A><H3>
+setAlignmentSelectionRenderer</H3>
+<PRE>
+public void <B>setAlignmentSelectionRenderer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A> selectionRenderer)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignmentSelectionRenderer()"><!-- --></A><H3>
+getAlignmentSelectionRenderer</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A> <B>getAlignmentSelectionRenderer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setCellHeight(int)"><!-- --></A><H3>
+setCellHeight</H3>
+<PRE>
+public void <B>setCellHeight</B>(int height)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellHeight()"><!-- --></A><H3>
+getCellHeight</H3>
+<PRE>
+public int <B>getCellHeight</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setCellWidth(int)"><!-- --></A><H3>
+setCellWidth</H3>
+<PRE>
+public void <B>setCellWidth</B>(int width)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellWidth()"><!-- --></A><H3>
+getCellWidth</H3>
+<PRE>
+public int <B>getCellWidth</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPreferredSize()"><!-- --></A><H3>
+getPreferredSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getPreferredSize</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getPreferredSize()">getPreferredSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMinimumSize()"><!-- --></A><H3>
+getMinimumSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getMinimumSize</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getMinimumSize()">getMinimumSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMaximumSize()"><!-- --></A><H3>
+getMaximumSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getMaximumSize</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getMaximumSize()">getMaximumSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setColorMap(uk.ac.man.bioinf.gui.color.ColorMap)"><!-- --></A><H3>
+setColorMap</H3>
+<PRE>
+public void <B>setColorMap</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> colorMap)</PRE>
+<DL>
+<DD>Changes the color map and notifies of change.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>colorMap</CODE> - the new color map</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColorMap()"><!-- --></A><H3>
+getColorMap</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/color/ColorMap.html">ColorMap</A> <B>getColorMap</B>()</PRE>
+<DL>
+<DD>Returns the current color map.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the color map</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setCursorModel(uk.ac.man.bioinf.gui.viewer.SequenceCursor)"><!-- --></A><H3>
+setCursorModel</H3>
+<PRE>
+public void <B>setCursorModel</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A> cursor)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCursorModel()"><!-- --></A><H3>
+getCursorModel</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A> <B>getCursorModel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addCursorChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+addCursorChangeListener</H3>
+<PRE>
+public void <B>addCursorChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeCursorChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+removeCursorChangeListener</H3>
+<PRE>
+public void <B>removeCursorChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+setPoint</H3>
+<PRE>
+public void <B>setPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMark()"><!-- --></A><H3>
+setMark</H3>
+<PRE>
+public void <B>setMark</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursor(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+moveCursor</H3>
+<PRE>
+public void <B>moveCursor</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> newPoint)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorUp(int)"><!-- --></A><H3>
+moveCursorUp</H3>
+<PRE>
+public void <B>moveCursorUp</B>(int number)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorDown(int)"><!-- --></A><H3>
+moveCursorDown</H3>
+<PRE>
+public void <B>moveCursorDown</B>(int number)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorPageUp()"><!-- --></A><H3>
+moveCursorPageUp</H3>
+<PRE>
+public void <B>moveCursorPageUp</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorPageDown()"><!-- --></A><H3>
+moveCursorPageDown</H3>
+<PRE>
+public void <B>moveCursorPageDown</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorBeginningOfAlignment()"><!-- --></A><H3>
+moveCursorBeginningOfAlignment</H3>
+<PRE>
+public void <B>moveCursorBeginningOfAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorEndOfAlignment()"><!-- --></A><H3>
+moveCursorEndOfAlignment</H3>
+<PRE>
+public void <B>moveCursorEndOfAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorRight(int)"><!-- --></A><H3>
+moveCursorRight</H3>
+<PRE>
+public void <B>moveCursorRight</B>(int number)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorLeft(int)"><!-- --></A><H3>
+moveCursorLeft</H3>
+<PRE>
+public void <B>moveCursorLeft</B>(int number)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorPageRight()"><!-- --></A><H3>
+moveCursorPageRight</H3>
+<PRE>
+public void <B>moveCursorPageRight</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorPageLeft()"><!-- --></A><H3>
+moveCursorPageLeft</H3>
+<PRE>
+public void <B>moveCursorPageLeft</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorBeginningOfSequence()"><!-- --></A><H3>
+moveCursorBeginningOfSequence</H3>
+<PRE>
+public void <B>moveCursorBeginningOfSequence</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorEndOfSequence()"><!-- --></A><H3>
+moveCursorEndOfSequence</H3>
+<PRE>
+public void <B>moveCursorEndOfSequence</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorToSequencePoint(int, int)"><!-- --></A><H3>
+moveCursorToSequencePoint</H3>
+<PRE>
+public void <B>moveCursorToSequencePoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="moveCursorToSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+moveCursorToSequencePoint</H3>
+<PRE>
+public void <B>moveCursorToSequencePoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPoint()"><!-- --></A><H3>
+getPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getPoint</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMark()"><!-- --></A><H3>
+getMark</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getMark</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequencePointAtPoint(int, int)"><!-- --></A><H3>
+getSequencePointAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getSequencePointAtPoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequencePointAtPoint(java.awt.Point)"><!-- --></A><H3>
+getSequencePointAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getSequencePointAtPoint</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPointAtSequencePoint(int, int)"><!-- --></A><H3>
+getPointAtSequencePoint</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> <B>getPointAtSequencePoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectangleForSequenceRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+getRectangleForSequenceRectangle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>getRectangleForSequenceRectangle</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> seqRect)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getCellBounds</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>getCellBounds</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="ensureSequencePointIsVisible(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+ensureSequencePointIsVisible</H3>
+<PRE>
+public void <B>ensureSequencePointIsVisible</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setReadonly(boolean)"><!-- --></A><H3>
+setReadonly</H3>
+<PRE>
+public void <B>setReadonly</B>(boolean readonly)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isReadonly()"><!-- --></A><H3>
+isReadonly</H3>
+<PRE>
+public boolean <B>isReadonly</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapsAt(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int)"><!-- --></A><H3>
+insertGapsAt</H3>
+<PRE>
+public void <B>insertGapsAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ int sizeOfGap)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapsAt(int, int, int)"><!-- --></A><H3>
+insertGapsAt</H3>
+<PRE>
+public void <B>insertGapsAt</B>(int x,
+ int y,
+ int sizeOfGap)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapsAt(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int)"><!-- --></A><H3>
+deleteGapsAt</H3>
+<PRE>
+public void <B>deleteGapsAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ int sizeOfGap)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapsAt(int, int, int)"><!-- --></A><H3>
+deleteGapsAt</H3>
+<PRE>
+public void <B>deleteGapsAt</B>(int x,
+ int y,
+ int sizeOfGap)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapsAtCursor(int)"><!-- --></A><H3>
+insertGapsAtCursor</H3>
+<PRE>
+public void <B>insertGapsAtCursor</B>(int sizeOfGap)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapsAtCursor(int)"><!-- --></A><H3>
+deleteGapsAtCursor</H3>
+<PRE>
+public void <B>deleteGapsAtCursor</B>(int sizeOfGap)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html">ReadonlyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVisibleSequenceRectangle()"><!-- --></A><H3>
+getVisibleSequenceRectangle</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getVisibleSequenceRectangle</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionModel()"><!-- --></A><H3>
+getSelectionModel</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> <B>getSelectionModel</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSelectionModel(uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel)"><!-- --></A><H3>
+setSelectionModel</H3>
+<PRE>
+public void <B>setSelectionModel</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A> selectionModel)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+extendSelection</H3>
+<PRE>
+public void <B>extendSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+stopSelection</H3>
+<PRE>
+public void <B>stopSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection()"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setSequenceAlignment</H3>
+<PRE>
+public void <B>setSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAlignment()"><!-- --></A><H3>
+getSequenceAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSequenceAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><!-- --></A><H3>
+valueChanged</H3>
+<PRE>
+public void <B>valueChanged</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPreferredScrollableViewportSize()"><!-- --></A><H3>
+getPreferredScrollableViewportSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getPreferredScrollableViewportSize</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollableUnitIncrement(java.awt.Rectangle, int, int)"><!-- --></A><H3>
+getScrollableUnitIncrement</H3>
+<PRE>
+public int <B>getScrollableUnitIncrement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> visibleRect,
+ int orientation,
+ int direction)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollableBlockIncrement(java.awt.Rectangle, int, int)"><!-- --></A><H3>
+getScrollableBlockIncrement</H3>
+<PRE>
+public int <B>getScrollableBlockIncrement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> visibleRect,
+ int orientation,
+ int direction)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollableTracksViewportWidth()"><!-- --></A><H3>
+getScrollableTracksViewportWidth</H3>
+<PRE>
+public boolean <B>getScrollableTracksViewportWidth</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getScrollableTracksViewportHeight()"><!-- --></A><H3>
+getScrollableTracksViewportHeight</H3>
+<PRE>
+public boolean <B>getScrollableTracksViewportHeight</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUIClassID()"><!-- --></A><H3>
+getUIClassID</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getUIClassID</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#getUIClassID()">getUIClassID</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setUI(uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI)"><!-- --></A><H3>
+setUI</H3>
+<PRE>
+public void <B>setUI</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A> ui)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="updateUI()"><!-- --></A><H3>
+updateUI</H3>
+<PRE>
+public void <B>updateUI</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#updateUI()">updateUI</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JAlignmentViewer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JComponent">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html
new file mode 100644
index 0000000..c2678f4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html
@@ -0,0 +1,386 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:14 BST 2002 -->
+<TITLE>
+JChangedScrollPane
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="JChangedScrollPane";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JChangedScrollPane.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JScrollPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JScrollPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.JScrollPane">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class JChangedScrollPane</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">javax.swing.JScrollPane</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.JChangedScrollPane</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>, <A HREF="ht [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>JChangedScrollPane</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></DL>
+
+<P>
+JChangedScrollPane.java
+
+
+ Created: Fri Mar 31 14:56:45 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: JChangedScrollPane.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.JChangedScrollPane">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.AccessibleJScrollPane.html">JScrollPane.AccessibleJScrollPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.ScrollBar.html">JScrollPane.ScrollBar</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#columnHeader">columnHeader</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#horizontalScrollBar">horizontalScrollBar</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#horizontalScrollBarPolicy">horizontalScrollBarPolicy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#lowerLeft" [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.ScrollPaneConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#COLUMN_HEADER">COLUMN_HEADER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#HORIZONTAL_SCROLLBAR">HORIZONTAL_SCROLLBAR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#HORIZONTAL_SCROLLBAR_ALWAYS">HORIZONTAL_SCROLLBAR_ALWAYS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html#JChangedScrollPane(java.awt.Component, int, int)">JChangedScrollPane</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html#JChangedScrollPane(javax.swing.ScrollPaneLayout, java.awt.Component, int, int)">JChangedScrollPane</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A> layout,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_javax.swing.JScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#createHorizontalScrollBar()">createHorizontalScrollBar</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#createVerticalScrollBar()">createVerticalScrollBar</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#createViewport()">createViewport</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPa [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="JChangedScrollPane(java.awt.Component, int, int)"><!-- --></A><H3>
+JChangedScrollPane</H3>
+<PRE>
+public <B>JChangedScrollPane</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JChangedScrollPane(javax.swing.ScrollPaneLayout, java.awt.Component, int, int)"><!-- --></A><H3>
+JChangedScrollPane</H3>
+<PRE>
+public <B>JChangedScrollPane</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A> layout,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JChangedScrollPane.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JScrollPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JScrollPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.JScrollPane">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html
new file mode 100644
index 0000000..17c6e1d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html
@@ -0,0 +1,391 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:14 BST 2002 -->
+<TITLE>
+JLayableScrollPane
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="JLayableScrollPane";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JLayableScrollPane.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JScrollPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JScrollPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.JScrollPane">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class JLayableScrollPane</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">javax.swing.JScrollPane</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.JLayableScrollPane</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>, <A HREF="ht [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>JLayableScrollPane</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></DL>
+
+<P>
+JLayableScrollPane.java
+
+ You cant reset the layout manager on a scroll pane, due to what
+ appears to be a bug in the JScrollPane layout, at least not it you
+ want anything to appear on screen. You cant reset the
+ layout manager on this class either. But you can specify what it is
+ in the constructor.
+
+ Created: Fri Mar 31 15:24:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: JLayableScrollPane.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.JLayableScrollPane">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.AccessibleJScrollPane.html">JScrollPane.AccessibleJScrollPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.ScrollBar.html">JScrollPane.ScrollBar</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#columnHeader">columnHeader</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#horizontalScrollBar">horizontalScrollBar</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#horizontalScrollBarPolicy">horizontalScrollBarPolicy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#lowerLeft" [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.ScrollPaneConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#COLUMN_HEADER">COLUMN_HEADER</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#HORIZONTAL_SCROLLBAR">HORIZONTAL_SCROLLBAR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html#HORIZONTAL_SCROLLBAR_ALWAYS">HORIZONTAL_SCROLLBAR_ALWAYS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html#JLayableScrollPane(java.awt.Component, int, int)">JLayableScrollPane</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html#JLayableScrollPane(javax.swing.ScrollPaneLayout, java.awt.Component, int, int)">JLayableScrollPane</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A> layout,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_javax.swing.JScrollPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html">JScrollPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#createHorizontalScrollBar()">createHorizontalScrollBar</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#createVerticalScrollBar()">createVerticalScrollBar</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html#createViewport()">createViewport</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPa [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="JLayableScrollPane(java.awt.Component, int, int)"><!-- --></A><H3>
+JLayableScrollPane</H3>
+<PRE>
+public <B>JLayableScrollPane</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="JLayableScrollPane(javax.swing.ScrollPaneLayout, java.awt.Component, int, int)"><!-- --></A><H3>
+JLayableScrollPane</H3>
+<PRE>
+public <B>JLayableScrollPane</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html">ScrollPaneLayout</A> layout,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> view,
+ int vsbPolicy,
+ int hsbPolicy)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="JLayableScrollPane.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JScrollPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JScrollPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.JScrollPane">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..3555e5f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:14 BST 2002 -->
+<TITLE>
+MultiplexerFastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="MultiplexerFastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MultiplexerFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class MultiplexerFastAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html">CursorLessFastAlignmentViewerCellRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>MultiplexerFastAlignmentViewerCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></DL>
+
+<P>
+MultiplexerFastAlignmentViewerCellRenderer.java
+
+ This multiplexer uses three other cell renderers to render the cell.
+ The reason for this is that as the size of the cell changes, it is
+ necessary to alter what is drawn.
+ <p>
+ As a result, this renderer listens to the
+ <code>JAlignmentViewer</code> for alterations to the size of the
+ cell.
+ <p>
+ The big disadvantage to this renderer may prove its downfall - it
+ has to make three function calls to draw the cell at normal size.
+
+ Created: Fri Sep 15 19:21:54 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: MultiplexerFastAlignmentViewerCellRenderer.java,v 1.6 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#MultiplexerFastAlignmentViewerCellRenderer(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">MultiplexerFastAlignmentViewerCellRenderer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#calculateViableRenderers(int)">calculateViableRenderers</A></B>(int cellSize)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MultiplexerFastAlignmentViewerCellRenderer(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+MultiplexerFastAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>MultiplexerFastAlignmentViewerCellRenderer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="calculateViableRenderers(int)"><!-- --></A><H3>
+calculateViableRenderers</H3>
+<PRE>
+protected void <B>calculateViableRenderers</B>(int cellSize)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignm [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>color</CODE> - the [...]
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MultiplexerFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html
new file mode 100644
index 0000000..2633a6b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html
@@ -0,0 +1,569 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:14 BST 2002 -->
+<TITLE>
+NullAlignmentSelectionModel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NullAlignmentSelectionModel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullAlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class NullAlignmentSelectionModel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NullAlignmentSelectionModel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></DL>
+
+<P>
+NullAlignmentSelectionModel.java
+
+ Trivial selection model. Returns 0 or false for everything,
+ and ignores selection events.
+
+
+ Created: Mon Jan 15 13:09:41 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NullAlignmentSelectionModel.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#clearSelection()">clearSelection</A></B>()</CODE>
+
+<BR>
+ Clear all the selections in this model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#clearSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">clearSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rectangle)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Start a selection at the given point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></B>()</CODE>
+
+<BR>
+ Returns the current selection or null if there is no
+ selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></B>()</CODE>
+
+<BR>
+ Get the number of selections.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get the first selection rectangle which surrounds the point, or
+ null if there is not one.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get all selection rectangles which surround this point, or null
+ if there is not one</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></B>(int index)</CODE>
+
+<BR>
+ Gets the given selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Is the point within one of the selection rectangles</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#isSelecting()">isSelecting</A></B>()</CODE>
+
+<BR>
+ is the current selection in the process of being selected.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Complete the selection at the given point</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isSelecting()"><!-- --></A><H3>
+isSelecting</H3>
+<PRE>
+public boolean <B>isSelecting</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>is the current selection in the process of being selected.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isSelecting()">isSelecting</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>true is selection is changing</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentSelection()"><!-- --></A><H3>
+getCurrentSelection</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getCurrentSelection</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Returns the current selection or null if there is no
+ selection. If there is more than one selection this should return
+ the most recently made selection
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSelections()"><!-- --></A><H3>
+getNumberSelections</H3>
+<PRE>
+public int <B>getNumberSelections</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get the number of selections.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of selections</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionAt(int)"><!-- --></A><H3>
+getSelectionAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSelectionAt</B>(int index)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ArrayIndexOutOfBoundsException.html">ArrayIndexOutOfBoundsException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Gets the given selection. The index should reflect the
+ chronological order in which the selections were made, with the
+ smallest index first
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index
+<DT><B>Returns:</B><DD>the selection array index at the given index
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ArrayIndexOutOfBoundsException.html">ArrayIndexOutOfBoundsException</A></CODE> - if the index is out of bounds</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+isPointSelected</H3>
+<PRE>
+public boolean <B>isPointSelected</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Is the point within one of the selection rectangles
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point
+<DT><B>Returns:</B><DD>true if point is within a rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection()"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Clear all the selections in this model
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#clearSelection()">clearSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rectangle)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectangleAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getRectangleAtPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get the first selection rectangle which surrounds the point, or
+ null if there is not one.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangle surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectanglesAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[] <B>getRectanglesAtPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get all selection rectangles which surround this point, or null
+ if there is not one
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangles surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+extendSelection</H3>
+<PRE>
+public void <B>extendSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Start a selection at the given point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the start of the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+stopSelection</H3>
+<PRE>
+public void <B>stopSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Complete the selection at the given point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point to complete the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+addAlignmentSelectionListener</H3>
+<PRE>
+public void <B>addAlignmentSelectionListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+removeAlignmentSelectionListener</H3>
+<PRE>
+public void <B>removeAlignmentSelectionListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullAlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html
new file mode 100644
index 0000000..d789155
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:15 BST 2002 -->
+<TITLE>
+PrintableAlignmentPanel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PrintableAlignmentPanel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PrintableAlignmentPanel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.JPanel">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class PrintableAlignmentPanel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">javax.swing.JPanel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PrintableAlignmentPanel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></DL>
+
+<P>
+PrintableAlignmentPanel.java
+
+
+ Created: Fri Mar 9 20:00:24 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PrintableAlignmentPanel.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.PrintableAlignmentPanel">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.AccessibleJPanel.html">JPanel.AccessibleJPanel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html#PrintableAlignmentPanel()">PrintableAlignmentPanel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUI()">getUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUIClassID()">getUIClassID</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#paramString()">paramString</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PrintableAlignmentPanel()"><!-- --></A><H3>
+PrintableAlignmentPanel</H3>
+<PRE>
+public <B>PrintableAlignmentPanel</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PrintableAlignmentPanel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.JPanel">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html
new file mode 100644
index 0000000..9e22e64
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html
@@ -0,0 +1,516 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:15 BST 2002 -->
+<TITLE>
+PrintableJAlignmentViewer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PrintableJAlignmentViewer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PrintableJAlignmentViewer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JComponent">NESTED</A> | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.gui.viewer.JAlignmentViewer">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class PrintableJAlignmentViewer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">uk.ac.man.bioinf.gui.viewer.JAlignmentViewer</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PrintableJAlignmentViewer</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html">Printable</A></DL>
+
+<P>
+PrintableJAlignmentViewer.java
+
+ A JAlignmentViewer which can be used to print
+
+ Created: Fri Mar 9 17:21:44 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PrintableJAlignmentViewer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.PrintableJAlignmentViewer">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.gui.viewer.JAlignmentViewer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#readonly">readonly</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#uiClassID">uiClassID</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.print.Printable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.print.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html">Printable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html#NO_SUCH_PAGE">NO_SUCH_PAGE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html#PAGE_EXISTS">PAGE_EXISTS</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#PrintableJAlignmentViewer(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">PrintableJAlignmentViewer</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#getCellsSquare()">getCellsSquare</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#print(java.awt.Graphics, java.awt.print.PageFormat, int)">print</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/PageFormat.html">PageFormat</A> pf,
+ int pi)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setCellsSquare(boolean)">setCellsSquare</A></B>(boolean square)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setJAlignmentViewer()">setJAlignmentViewer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setXCellsPerPage(int)">setXCellsPerPage</A></B>(int cells)</CODE>
+
+<BR>
+ Set the number of cells which should be drawn across each page.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html#setYCellsPerPage(int)">setYCellsPerPage</A></B>(int cells)</CODE>
+
+<BR>
+ Set the number of cells which should be drawn down each page.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.JAlignmentViewer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#addCursorChangeListener(javax.swing.event.ChangeListener)">addCursorChangeListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A>, <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">change [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PrintableJAlignmentViewer(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+PrintableJAlignmentViewer</H3>
+<PRE>
+public <B>PrintableJAlignmentViewer</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setJAlignmentViewer()"><!-- --></A><H3>
+setJAlignmentViewer</H3>
+<PRE>
+public void <B>setJAlignmentViewer</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setXCellsPerPage(int)"><!-- --></A><H3>
+setXCellsPerPage</H3>
+<PRE>
+public void <B>setXCellsPerPage</B>(int cells)</PRE>
+<DL>
+<DD>Set the number of cells which should be drawn across each page. This
+ method is probably a lot more useful than cell width which is a
+ bit blank.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>cells</CODE> - the number of cells per page</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setYCellsPerPage(int)"><!-- --></A><H3>
+setYCellsPerPage</H3>
+<PRE>
+public void <B>setYCellsPerPage</B>(int cells)</PRE>
+<DL>
+<DD>Set the number of cells which should be drawn down each page. If
+ the total size of the alignment is too big to fit, then multiple
+ pages will have to be used. <p>
+
+ If the method <code>getCellsSquare</code> returns true then this
+ property will be ignored in preference to XCellsPerPage.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>cells</CODE> - an <code>int</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setCellsSquare(boolean)"><!-- --></A><H3>
+setCellsSquare</H3>
+<PRE>
+public void <B>setCellsSquare</B>(boolean square)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellsSquare()"><!-- --></A><H3>
+getCellsSquare</H3>
+<PRE>
+public boolean <B>getCellsSquare</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="print(java.awt.Graphics, java.awt.print.PageFormat, int)"><!-- --></A><H3>
+print</H3>
+<PRE>
+public int <B>print</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/PageFormat.html">PageFormat</A> pf,
+ int pi)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/PrinterException.html">PrinterException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>print</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html">Printable</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/PrinterException.html">PrinterException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PrintableJAlignmentViewer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JComponent">NESTED</A> | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.gui.viewer.JAlignmentViewer">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ReadonlyException.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ReadonlyException.html
new file mode 100644
index 0000000..8e827f3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/ReadonlyException.html
@@ -0,0 +1,319 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+ReadonlyException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ReadonlyException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ReadonlyException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class ReadonlyException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.ReadonlyException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ReadonlyException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+ReadonlyException.java
+
+
+ Created: Thu Dec 14 15:40:59 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ReadonlyException.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.ReadonlyException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException()">ReadonlyException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">ReadonlyException</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> jav)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException(java.lang.String)">ReadonlyException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#ReadonlyException(java.lang.String, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">ReadonlyException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> jav)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html#getViewer()">getViewer</A></B>()</CODE>
+
+<BR>
+ Returns the <code>JAlignmentViewer</code> that caused the
+ exception, or null if the exception came from elsewhere.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ReadonlyException()"><!-- --></A><H3>
+ReadonlyException</H3>
+<PRE>
+public <B>ReadonlyException</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ReadonlyException(java.lang.String)"><!-- --></A><H3>
+ReadonlyException</H3>
+<PRE>
+public <B>ReadonlyException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ReadonlyException(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+ReadonlyException</H3>
+<PRE>
+public <B>ReadonlyException</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> jav)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ReadonlyException(java.lang.String, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+ReadonlyException</H3>
+<PRE>
+public <B>ReadonlyException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> jav)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getViewer()"><!-- --></A><H3>
+getViewer</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> <B>getViewer</B>()</PRE>
+<DL>
+<DD>Returns the <code>JAlignmentViewer</code> that caused the
+ exception, or null if the exception came from elsewhere.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the alignment viewer<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><CODE>JAlignmentViewer</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ReadonlyException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/SequenceCursor.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/SequenceCursor.html
new file mode 100644
index 0000000..4c6ef7c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/SequenceCursor.html
@@ -0,0 +1,323 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:56 BST 2002 -->
+<TITLE>
+SequenceCursor
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceCursor";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceCursor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Interface SequenceCursor</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html">DefaultSequenceCursor</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceCursor</B></DL>
+
+<P>
+SequenceCursor.java
+
+
+ Created: Mon Apr 3 18:59:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceCursor.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#addChangeListener(javax.swing.event.ChangeListener)">addChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ Add a listener to this cursor</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#getMark()">getMark</A></B>()</CODE>
+
+<BR>
+ Returns the position of mark</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#getPoint()">getPoint</A></B>()</CODE>
+
+<BR>
+ Returns the position of point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#removeChangeListener(javax.swing.event.ChangeListener)">removeChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ Remove the listener from this cursor</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#setMark()">setMark</A></B>()</CODE>
+
+<BR>
+ Set the mark to the current position of point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html#setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">setPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> position)</CODE>
+
+<BR>
+ Set the point to the new position</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+addChangeListener</H3>
+<PRE>
+public void <B>addChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD>Add a listener to this cursor
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to add</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+removeChangeListener</H3>
+<PRE>
+public void <B>removeChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD>Remove the listener from this cursor
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to remove</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+setPoint</H3>
+<PRE>
+public void <B>setPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> position)</PRE>
+<DL>
+<DD>Set the point to the new position
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>position</CODE> - the position to set</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setMark()"><!-- --></A><H3>
+setMark</H3>
+<PRE>
+public void <B>setMark</B>()</PRE>
+<DL>
+<DD>Set the mark to the current position of point
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPoint()"><!-- --></A><H3>
+getPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getPoint</B>()</PRE>
+<DL>
+<DD>Returns the position of point
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the position</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMark()"><!-- --></A><H3>
+getMark</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getMark</B>()</PRE>
+<DL>
+<DD>Returns the position of mark
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the position</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceCursor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html
new file mode 100644
index 0000000..13d19c6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html
@@ -0,0 +1,549 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:16 BST 2002 -->
+<TITLE>
+SingleAlignmentSelectionModel
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SingleAlignmentSelectionModel";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleAlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class SingleAlignmentSelectionModel</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SingleAlignmentSelectionModel</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></DL>
+
+<P>
+SingleAlignmentSelectionModel.java
+
+
+ Created: Mon Apr 10 11:59:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SingleAlignmentSelectionModel.java,v 1.5 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#SingleAlignmentSelectionModel()">SingleAlignmentSelectionModel</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#clearSelection()">clearSelection</A></B>()</CODE>
+
+<BR>
+ Clear all the selections in this model</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Start a selection at the given point</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></B>()</CODE>
+
+<BR>
+ Returns the current selection or null if there is no
+ selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></B>()</CODE>
+
+<BR>
+ Get the number of selections.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get the first selection rectangle which surrounds the point, or
+ null if there is not one.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Get all selection rectangles which surround this point, or null
+ if there is not one</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></B>(int index)</CODE>
+
+<BR>
+ Gets the given selection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Is the point within one of the selection rectangles</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#isSelecting()">isSelecting</A></B>()</CODE>
+
+<BR>
+ is the current selection in the process of being selected.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Complete the selection at the given point</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SingleAlignmentSelectionModel()"><!-- --></A><H3>
+SingleAlignmentSelectionModel</H3>
+<PRE>
+public <B>SingleAlignmentSelectionModel</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isSelecting()"><!-- --></A><H3>
+isSelecting</H3>
+<PRE>
+public boolean <B>isSelecting</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>is the current selection in the process of being selected.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isSelecting()">isSelecting</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>true is selection is changing</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCurrentSelection()"><!-- --></A><H3>
+getCurrentSelection</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getCurrentSelection</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Returns the current selection or null if there is no
+ selection. If there is more than one selection this should return
+ the most recently made selection
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getCurrentSelection()">getCurrentSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSelections()"><!-- --></A><H3>
+getNumberSelections</H3>
+<PRE>
+public int <B>getNumberSelections</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get the number of selections.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getNumberSelections()">getNumberSelections</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of selections</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSelectionAt(int)"><!-- --></A><H3>
+getSelectionAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSelectionAt</B>(int index)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ArrayIndexOutOfBoundsException.html">ArrayIndexOutOfBoundsException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Gets the given selection. The index should reflect the
+ chronological order in which the selections were made, with the
+ smallest index first
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getSelectionAt(int)">getSelectionAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index
+<DT><B>Returns:</B><DD>the selection array index at the given index
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/ArrayIndexOutOfBoundsException.html">ArrayIndexOutOfBoundsException</A></CODE> - if the index is out of bounds</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+isPointSelected</H3>
+<PRE>
+public boolean <B>isPointSelected</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Is the point within one of the selection rectangles
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#isPointSelected(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">isPointSelected</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point
+<DT><B>Returns:</B><DD>true if point is within a rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSelection()"><!-- --></A><H3>
+clearSelection</H3>
+<PRE>
+public void <B>clearSelection</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Clear all the selections in this model
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#clearSelection()">clearSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectangleAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getRectangleAtPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get the first selection rectangle which surrounds the point, or
+ null if there is not one.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectangleAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectangleAtPoint</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangle surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getRectanglesAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A>[] <B>getRectanglesAtPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Get all selection rectangles which surround this point, or null
+ if there is not one
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#getRectanglesAtPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getRectanglesAtPoint</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in question
+<DT><B>Returns:</B><DD>the rectangles surrounding point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+extendSelection</H3>
+<PRE>
+public void <B>extendSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Start a selection at the given point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#extendSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">extendSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the start of the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+stopSelection</H3>
+<PRE>
+public void <B>stopSelection</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></B></DD>
+<DD>Complete the selection at the given point
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#stopSelection(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">stopSelection</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point to complete the selection</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+addAlignmentSelectionListener</H3>
+<PRE>
+public void <B>addAlignmentSelectionListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+removeAlignmentSelectionListener</H3>
+<PRE>
+public void <B>removeAlignmentSelectionListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleAlignmentSelectionModel.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html
new file mode 100644
index 0000000..7f53189
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:16 BST 2002 -->
+<TITLE>
+TextFastAlignmentViewerCellRenderer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="TextFastAlignmentViewerCellRenderer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="TextFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer</FONT>
+<BR>
+Class TextFastAlignmentViewerCellRenderer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.TextFastAlignmentViewerCellRenderer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>TextFastAlignmentViewerCellRenderer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></DL>
+
+<P>
+TextFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer. This one deals specifically with drawing the
+ character of the element in the cell.
+ <p>
+ By default, this will probably be drawn last, although this is
+ determined by the RendererManager.
+
+ Created: Fri Aug 25 15:11:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: TextFastAlignmentViewerCellRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html#TextFastAlignmentViewerCellRenderer()">TextFastAlignmentViewerCellRenderer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</CODE>
+
+<BR>
+ This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="TextFastAlignmentViewerCellRenderer()"><!-- --></A><H3>
+TextFastAlignmentViewerCellRenderer</H3>
+<PRE>
+public <B>TextFastAlignmentViewerCellRenderer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)"><!-- --></A><H3>
+renderAlignmentViewerCell</H3>
+<PRE>
+public void <B>renderAlignmentViewerCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int x,
+ int y,
+ int width,
+ int height,
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> location,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Color.html">Color</A> color,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoint)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A></CODE></B></DD>
+<DD>This method renders the cell at the given location in a graphics
+ object, with reference to the JAlignmentViewer. It makes use of
+ certain parameters, such as the color of the element being
+ drawn.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html#renderAlignmentViewerCell(java.awt.Graphics, int, int, int, int, uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, uk.ac.man.bioinf.sequence.Element, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Color, boolean, boolean, boolean)">renderAlignmentViewerCell</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignm [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>g</CODE> - the graphics object in use<DD><CODE>x</CODE> - the 'x' location in the graphical display<DD><CODE>y</CODE> - the 'y' location in the graphical display<DD><CODE>width</CODE> - the width of the cell<DD><CODE>height</CODE> - the height of the cell<DD><CODE>viewer</CODE> - the JAlignmentViewer object<DD><CODE>element</CODE> - the element being drawn<DD><CODE>location</CODE> - the sequence alignment location of the element<DD><CODE>color</CODE> - the [...]
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="TextFastAlignmentViewerCellRenderer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html
new file mode 100644
index 0000000..e70238b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html
@@ -0,0 +1,327 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+AlignmentSelectionEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentSelectionEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.event</FONT>
+<BR>
+Class AlignmentSelectionEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignmentSelectionEvent</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></DL>
+
+<P>
+AlignmentSelectionEvent.java
+
+
+ Created: Mon Apr 10 12:22:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentSelectionEvent.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#AlignmentSelectionEvent(java.lang.Object, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle, boolean)">AlignmentSelectionEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rectangle,
+ boolean isAdjusting)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#getSelectionRectangle()">getSelectionRectangle</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#isValueAdjusting()">isValueAdjusting</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentSelectionEvent(java.lang.Object, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle, boolean)"><!-- --></A><H3>
+AlignmentSelectionEvent</H3>
+<PRE>
+public <B>AlignmentSelectionEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rectangle,
+ boolean isAdjusting)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSelectionRectangle()"><!-- --></A><H3>
+getSelectionRectangle</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSelectionRectangle</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isValueAdjusting()"><!-- --></A><H3>
+isValueAdjusting</H3>
+<PRE>
+public boolean <B>isValueAdjusting</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html
new file mode 100644
index 0000000..4d050a9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+AlignmentSelectionListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentSelectionListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.event</FONT>
+<BR>
+Interface AlignmentSelectionListener</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.html">CinemaMotifFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.html">NamedAlignmentSelectionModel</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentSelectionListener</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DL>
+
+<P>
+AlignmentSelectionListener.java
+
+
+ Created: Mon Apr 10 12:12:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentSelectionListener.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html#valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">valueChanged</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="valueChanged(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><!-- --></A><H3>
+valueChanged</H3>
+<PRE>
+public void <B>valueChanged</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html
new file mode 100644
index 0000000..e4f2d84
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html
@@ -0,0 +1,290 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+AlignmentSelectionListenerSupport
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentSelectionListenerSupport";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.event</FONT>
+<BR>
+Class AlignmentSelectionListenerSupport</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignmentSelectionListenerSupport</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AlignmentSelectionListenerSupport.java
+
+
+ Created: Mon Apr 10 12:31:19 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentSelectionListenerSupport.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#AlignmentSelectionListenerSupport()">AlignmentSelectionListenerSupport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">addAlignmentSelectionListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#fireAlignmentSelectionEvent(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)">fireAlignmentSelectionEvent</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html#removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)">removeAlignmentSelectionListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentSelectionListenerSupport()"><!-- --></A><H3>
+AlignmentSelectionListenerSupport</H3>
+<PRE>
+public <B>AlignmentSelectionListenerSupport</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+addAlignmentSelectionListener</H3>
+<PRE>
+public void <B>addAlignmentSelectionListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentSelectionListener(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener)"><!-- --></A><H3>
+removeAlignmentSelectionListener</H3>
+<PRE>
+public void <B>removeAlignmentSelectionListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireAlignmentSelectionEvent(uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent)"><!-- --></A><H3>
+fireAlignmentSelectionEvent</H3>
+<PRE>
+public void <B>fireAlignmentSelectionEvent</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html">AlignmentSelectionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentSelectionListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html
new file mode 100644
index 0000000..dd9a74b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html
@@ -0,0 +1,290 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+ChangeListenerSupport
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ChangeListenerSupport";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.event</FONT>
+<BR>
+Class ChangeListenerSupport</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ChangeListenerSupport</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ChangeListenerSupport.java
+
+
+ Created: Tue Apr 4 13:31:52 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ChangeListenerSupport.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#ChangeListenerSupport()">ChangeListenerSupport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#addChangeListener(javax.swing.event.ChangeListener)">addChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#fireChangeEvent(javax.swing.event.ChangeEvent)">fireChangeEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeEvent.html">ChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html#removeChangeListener(javax.swing.event.ChangeListener)">removeChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ChangeListenerSupport()"><!-- --></A><H3>
+ChangeListenerSupport</H3>
+<PRE>
+public <B>ChangeListenerSupport</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+addChangeListener</H3>
+<PRE>
+public void <B>addChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeChangeListener(javax.swing.event.ChangeListener)"><!-- --></A><H3>
+removeChangeListener</H3>
+<PRE>
+public void <B>removeChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireChangeEvent(javax.swing.event.ChangeEvent)"><!-- --></A><H3>
+fireChangeEvent</H3>
+<PRE>
+public void <B>fireChangeEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeEvent.html">ChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-frame.html
new file mode 100644
index 0000000..79d5bf7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-frame.html
@@ -0,0 +1,47 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.event()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.event()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.viewer.event</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentSelectionListener.html" TARGET="classFrame"><I>AlignmentSelectionListener</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentSelectionEvent.html" TARGET="classFrame">AlignmentSelectionEvent</A>
+<BR>
+<A HREF="AlignmentSelectionListenerSupport.html" TARGET="classFrame">AlignmentSelectionListenerSupport</A>
+<BR>
+<A HREF="ChangeListenerSupport.html" TARGET="classFrame">ChangeListenerSupport</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-summary.html
new file mode 100644
index 0000000..cac53ab
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-summary.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.event()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.event()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.viewer.event
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentSelectionListener.html"><I>AlignmentSelectionListener</I></A></B></TD>
+<TD>AlignmentSelectionListener.java
+
+
+ Created: Mon Apr 10 12:12:33 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentSelectionEvent.html">AlignmentSelectionEvent</A></B></TD>
+<TD>AlignmentSelectionEvent.java
+
+
+ Created: Mon Apr 10 12:22:22 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentSelectionListenerSupport.html">AlignmentSelectionListenerSupport</A></B></TD>
+<TD>AlignmentSelectionListenerSupport.java
+
+
+ Created: Mon Apr 10 12:31:19 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ChangeListenerSupport.html">ChangeListenerSupport</A></B></TD>
+<TD>ChangeListenerSupport.java
+
+
+ Created: Tue Apr 4 13:31:52 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-tree.html
new file mode 100644
index 0000000..99feff8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/event/package-tree.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.event Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.event Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.viewer.event
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.html"><B>AlignmentSelectionListenerSupport</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.html"><B>ChangeListenerSupport</B></A><LI TYPE="circle">class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Event [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.html"><B>AlignmentSelectionEvent</B></A></UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html"><B>EventListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html"><B>AlignmentSelectionListener</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-frame.html
new file mode 100644
index 0000000..bae57f4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-frame.html
@@ -0,0 +1,102 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.viewer</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentSelectionModel.html" TARGET="classFrame"><I>AlignmentSelectionModel</I></A>
+<BR>
+<A HREF="AlignmentSelectionRenderer.html" TARGET="classFrame"><I>AlignmentSelectionRenderer</I></A>
+<BR>
+<A HREF="AlignmentViewerCellRenderer.html" TARGET="classFrame"><I>AlignmentViewerCellRenderer</I></A>
+<BR>
+<A HREF="FastAlignmentViewerCellRenderer.html" TARGET="classFrame"><I>FastAlignmentViewerCellRenderer</I></A>
+<BR>
+<A HREF="SequenceCursor.html" TARGET="classFrame"><I>SequenceCursor</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="BorderFastAlignmentViewerCellRenderer.html" TARGET="classFrame">BorderFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="ButtonViewerPopupMenu.html" TARGET="classFrame">ButtonViewerPopupMenu</A>
+<BR>
+<A HREF="ColorFastAlignmentViewerCellRenderer.html" TARGET="classFrame">ColorFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="CursorLessFastAlignmentViewerCellRenderer.html" TARGET="classFrame">CursorLessFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="DefaultAlignmentSelectionRenderer.html" TARGET="classFrame">DefaultAlignmentSelectionRenderer</A>
+<BR>
+<A HREF="DefaultAlignmentViewerCellRenderer.html" TARGET="classFrame">DefaultAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="DefaultFastAlignmentViewerCellRenderer.html" TARGET="classFrame">DefaultFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="DefaultSequenceCursor.html" TARGET="classFrame">DefaultSequenceCursor</A>
+<BR>
+<A HREF="Install.html" TARGET="classFrame">Install</A>
+<BR>
+<A HREF="InvertedScrollPaneLayout.html" TARGET="classFrame">InvertedScrollPaneLayout</A>
+<BR>
+<A HREF="JAlignmentButtonPanel.html" TARGET="classFrame">JAlignmentButtonPanel</A>
+<BR>
+<A HREF="JAlignmentRuler.html" TARGET="classFrame">JAlignmentRuler</A>
+<BR>
+<A HREF="JAlignmentViewer.html" TARGET="classFrame">JAlignmentViewer</A>
+<BR>
+<A HREF="JChangedScrollPane.html" TARGET="classFrame">JChangedScrollPane</A>
+<BR>
+<A HREF="JLayableScrollPane.html" TARGET="classFrame">JLayableScrollPane</A>
+<BR>
+<A HREF="MultiplexerFastAlignmentViewerCellRenderer.html" TARGET="classFrame">MultiplexerFastAlignmentViewerCellRenderer</A>
+<BR>
+<A HREF="NullAlignmentSelectionModel.html" TARGET="classFrame">NullAlignmentSelectionModel</A>
+<BR>
+<A HREF="PrintableAlignmentPanel.html" TARGET="classFrame">PrintableAlignmentPanel</A>
+<BR>
+<A HREF="PrintableJAlignmentViewer.html" TARGET="classFrame">PrintableJAlignmentViewer</A>
+<BR>
+<A HREF="SingleAlignmentSelectionModel.html" TARGET="classFrame">SingleAlignmentSelectionModel</A>
+<BR>
+<A HREF="TextFastAlignmentViewerCellRenderer.html" TARGET="classFrame">TextFastAlignmentViewerCellRenderer</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ReadonlyException.html" TARGET="classFrame">ReadonlyException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-summary.html
new file mode 100644
index 0000000..ab8ccd9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-summary.html
@@ -0,0 +1,341 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.viewer
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentSelectionModel.html"><I>AlignmentSelectionModel</I></A></B></TD>
+<TD>AlignmentSelectionModel.java
+
+ This defines the selection model for the JAlignmentViewer.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentSelectionRenderer.html"><I>AlignmentSelectionRenderer</I></A></B></TD>
+<TD>SelectionRenderer.java
+
+
+ Created: Wed Mar 7 18:45:50 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentViewerCellRenderer.html"><I>AlignmentViewerCellRenderer</I></A></B></TD>
+<TD>AlignmentViewerCellRenderer.java
+
+ Initial interface for the AlignmentViewerCellRender.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FastAlignmentViewerCellRenderer.html"><I>FastAlignmentViewerCellRenderer</I></A></B></TD>
+<TD>FastAlignmentViewerCellRenderer.java
+
+ Although the JAlignmentViewer provides a pluggable renderer
+ architecture with the AlignmentViewerCellRenderer it has been found
+ that this has a fairly disasterous effect on performance of the
+ viewer particularly with respect to scrolling, due to the large
+ number of method calls and events to render a cell.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceCursor.html"><I>SequenceCursor</I></A></B></TD>
+<TD>SequenceCursor.java
+
+
+ Created: Mon Apr 3 18:59:26 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="BorderFastAlignmentViewerCellRenderer.html">BorderFastAlignmentViewerCellRenderer</A></B></TD>
+<TD>BorderFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ButtonViewerPopupMenu.html">ButtonViewerPopupMenu</A></B></TD>
+<TD>ButtonViewerPopupMenu.java
+
+ This class implements a pop up menu for the
+ JAlignmentButtonPanel.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ColorFastAlignmentViewerCellRenderer.html">ColorFastAlignmentViewerCellRenderer</A></B></TD>
+<TD>ColorFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CursorLessFastAlignmentViewerCellRenderer.html">CursorLessFastAlignmentViewerCellRenderer</A></B></TD>
+<TD>CursorLessFastAlignmentViewerCellRenderer.java
+
+
+ Created: Thu Jul 13 17:59:36 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultAlignmentSelectionRenderer.html">DefaultAlignmentSelectionRenderer</A></B></TD>
+<TD>DefaultAlignmentSelectionRenderer.java
+
+
+ Created: Wed Mar 7 18:59:56 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultAlignmentViewerCellRenderer.html">DefaultAlignmentViewerCellRenderer</A></B></TD>
+<TD>DefaultAlignmentViewerCellRenderer.java
+
+
+ Created: Mon Mar 20 20:23:12 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultFastAlignmentViewerCellRenderer.html">DefaultFastAlignmentViewerCellRenderer</A></B></TD>
+<TD>DefaultFastAlignmentViewerCellRenderer.java
+
+
+ Created: Mon Apr 17 20:11:46 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultSequenceCursor.html">DefaultSequenceCursor</A></B></TD>
+<TD>DefaultSequenceCursor.java
+
+
+ Created: Tue Apr 4 12:49:30 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Install.html">Install</A></B></TD>
+<TD>Install.java
+
+ This class provides the install information for the all of the
+ classes in the viewer package.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvertedScrollPaneLayout.html">InvertedScrollPaneLayout</A></B></TD>
+<TD>InvertedScrollPaneLayout.java
+
+
+ Created: Fri Mar 31 14:27:41 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="JAlignmentButtonPanel.html">JAlignmentButtonPanel</A></B></TD>
+<TD>JAlignmentButtonPanel.java
+
+ This component provides a rank of Buttons relating to a
+ SequenceAlignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="JAlignmentRuler.html">JAlignmentRuler</A></B></TD>
+<TD>JAlignmentRuler.java
+
+
+
+ Created: Thu Mar 23 12:33:50 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="JAlignmentViewer.html">JAlignmentViewer</A></B></TD>
+<TD>JAlignmentViewer.java
+
+
+ Created: Tue Mar 14 16:28:59 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="JChangedScrollPane.html">JChangedScrollPane</A></B></TD>
+<TD>JChangedScrollPane.java
+
+
+ Created: Fri Mar 31 14:56:45 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="JLayableScrollPane.html">JLayableScrollPane</A></B></TD>
+<TD>JLayableScrollPane.java
+
+ You cant reset the layout manager on a scroll pane, due to what
+ appears to be a bug in the JScrollPane layout, at least not it you
+ want anything to appear on screen.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MultiplexerFastAlignmentViewerCellRenderer.html">MultiplexerFastAlignmentViewerCellRenderer</A></B></TD>
+<TD>MultiplexerFastAlignmentViewerCellRenderer.java
+
+ This multiplexer uses three other cell renderers to render the cell.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NullAlignmentSelectionModel.html">NullAlignmentSelectionModel</A></B></TD>
+<TD>NullAlignmentSelectionModel.java
+
+ Trivial selection model.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PrintableAlignmentPanel.html">PrintableAlignmentPanel</A></B></TD>
+<TD>PrintableAlignmentPanel.java
+
+
+ Created: Fri Mar 9 20:00:24 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PrintableJAlignmentViewer.html">PrintableJAlignmentViewer</A></B></TD>
+<TD>PrintableJAlignmentViewer.java
+
+ A JAlignmentViewer which can be used to print
+
+ Created: Fri Mar 9 17:21:44 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SingleAlignmentSelectionModel.html">SingleAlignmentSelectionModel</A></B></TD>
+<TD>SingleAlignmentSelectionModel.java
+
+
+ Created: Mon Apr 10 11:59:44 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="TextFastAlignmentViewerCellRenderer.html">TextFastAlignmentViewerCellRenderer</A></B></TD>
+<TD>TextFastAlignmentViewerCellRenderer.java
+
+ One of three classes designed to render cells in the
+ JAlignmentViewer.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ReadonlyException.html">ReadonlyException</A></B></TD>
+<TD>ReadonlyException.java
+
+
+ Created: Thu Dec 14 15:40:59 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-tree.html
new file mode 100644
index 0000000..5e27c03
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/package-tree.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:11 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.viewer
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.html"><B>BorderFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.html"><B>ColorFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html"><B>JAlignmentViewer</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.gui.viewer.event.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.html">AlignmentSelectionListener</A>, uk.a [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.html"><B>PrintableJAlignmentViewer</B></A> (implements java.awt.print.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/print/Printable.html">Printable</A>)
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JLabel.html"><B>JLabel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.html"><B>DefaultAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.html">AlignmentViewerCellRenderer</A>)
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html"><B>JPanel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.html"><B>JAlignmentButtonPanel</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/ItemSelectable.html">ItemSelectable</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.html"><B>PrintableAlignmentPanel</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPopupMenu.html"><B>JPopupMenu</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/MenuElement.html">MenuElement</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.html"><B>ButtonViewerPopupMenu</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A>)
+</UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JScrollPane.html"><B>JScrollPane</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.html"><B>JChangedScrollPane</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.html"><B>JLayableScrollPane</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JSlider.html"><B>JSlider</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/SwingConstants.html">SwingConstants</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.html"><B>JAlignmentRuler</B></A></UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.html"><B>DefaultAlignmentSelectionRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html">AlignmentSelectionRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.html"><B>DefaultFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.html"><B>DefaultSequenceCursor</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SequenceCursor.html">SequenceCursor</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/Install.html"><B>Install</B></A> (implements java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.html"><B>MultiplexerFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">Proper [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.html"><B>CursorLessFastAlignmentViewerCellRenderer</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.html"><B>NullAlignmentSelectionModel</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>)
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneLayout.html"><B>ScrollPaneLayout</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/LayoutManager.html">LayoutManager</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/ScrollPaneConstants.html">ScrollPaneConstants</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable. [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.html"><B>InvertedScrollPaneLayout</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.html"><B>SingleAlignmentSelectionModel</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html">AlignmentSelectionModel</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.html"><B>TextFastAlignmentViewerCellRenderer</B></A> (implements uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.html">FastAlignmentViewerCellRenderer</A>)
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/ReadonlyException.html"><B>ReadonlyException</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.html"><B>AlignmentSelectionModel</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.html"><B>AlignmentSelectionRenderer</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.gui.viewer.<A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRender [...]
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/util/forms/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html
new file mode 100644
index 0000000..09fb1fe
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html
@@ -0,0 +1,231 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+AlignmentRulerUI
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentRulerUI";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentRulerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.plaf.ComponentUI">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class AlignmentRulerUI</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">javax.swing.plaf.ComponentUI</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.AlignmentRulerUI</B>
+</PRE>
+<HR>
+<DL>
+<DT>public abstract class <B>AlignmentRulerUI</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></DL>
+
+<P>
+AlignmentRulerUI.java
+
+
+ Created: Thu Mar 23 17:10:05 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentRulerUI.java,v 1.2 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html#AlignmentRulerUI()">AlignmentRulerUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_javax.swing.plaf.ComponentUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#contains(javax.swing.JComponent, int, int)">contains</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#createUI(javax.swing.JComponent)">createUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChild(javax.swing.JComponent, int)">getAccessibleChild</A>, <A HREF="http://java.sun.com/product [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentRulerUI()"><!-- --></A><H3>
+AlignmentRulerUI</H3>
+<PRE>
+public <B>AlignmentRulerUI</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentRulerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_javax.swing.plaf.ComponentUI">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html
new file mode 100644
index 0000000..a214db9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html
@@ -0,0 +1,346 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+AlignmentViewerUI
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentViewerUI";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentViewerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class AlignmentViewerUI</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">javax.swing.plaf.ComponentUI</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AlignmentViewerUI</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></DL>
+
+<P>
+AlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:29:34 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentViewerUI.java,v 1.4 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#AlignmentViewerUI()">AlignmentViewerUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getCellBounds</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getPointAtSequencePoint(int, int)">getPointAtSequencePoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getPointAtSequencePoint</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(int, int)">getSequencePointAtPoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(java.awt.Point)">getSequencePointAtPoint</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.ComponentUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#contains(javax.swing.JComponent, int, int)">contains</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#createUI(javax.swing.JComponent)">createUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChild(javax.swing.JComponent, int)">getAccessibleChild</A>, <A HREF="http://java.sun.com/product [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentViewerUI()"><!-- --></A><H3>
+AlignmentViewerUI</H3>
+<PRE>
+public <B>AlignmentViewerUI</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSequencePointAtPoint(int, int)"><!-- --></A><H3>
+getSequencePointAtPoint</H3>
+<PRE>
+public abstract <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getSequencePointAtPoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequencePointAtPoint(java.awt.Point)"><!-- --></A><H3>
+getSequencePointAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getSequencePointAtPoint</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPointAtSequencePoint(int, int)"><!-- --></A><H3>
+getPointAtSequencePoint</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> <B>getPointAtSequencePoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getPointAtSequencePoint</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> <B>getPointAtSequencePoint</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getCellBounds</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>getCellBounds</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentViewerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html
new file mode 100644
index 0000000..065f6eb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html
@@ -0,0 +1,508 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:17 BST 2002 -->
+<TITLE>
+BasicAlignmentRulerUI
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicAlignmentRulerUI";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentRulerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class BasicAlignmentRulerUI</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">javax.swing.plaf.ComponentUI</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/SliderUI.html">javax.swing.plaf.SliderUI</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">javax.swing.plaf.basic.BasicSliderUI</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>BasicAlignmentRulerUI</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></DL>
+
+<P>
+BasicAlignmentRulerUI.java
+
+
+ Created: Thu Mar 23 17:10:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: BasicAlignmentRulerUI.java,v 1.3 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.ActionScroller.html">BasicSliderUI.ActionScroller</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.ChangeHandler.html">BasicSliderUI.ChangeHandler</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.ComponentHandler.html">BasicSliderUI.ComponentHandler</A>, <A HREF="http://java.sun.com/products/j [...]
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#changeListener">changeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#componentListener">componentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#contentRect">contentRect</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/Basic [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#BasicAlignmentRulerUI(javax.swing.JComponent)">BasicAlignmentRulerUI</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateGeometry()">calculateGeometry</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateThumbLocation()">calculateThumbLocation</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateTrackBuffer()">calculateTrackBuffer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#calculateTrackRect()">calculateTrackRect</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#createUI(javax.swing.JComponent)">createUI</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#getPreferredSize(javax.swing.JComponent)">getPreferredSize</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#paint(java.awt.Graphics, javax.swing.JComponent)">paint</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#paintThumb(java.awt.Graphics)">paintThumb</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#paintTrack(java.awt.Graphics)">paintTrack</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html#recalculateIfInsetsChanged()">recalculateIfInsetsChanged</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateContentRect()">calculateContentRect</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateFocusRect()">calculateFocusRect</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateLabelRect()">calculateLabelRect</A>, <A HREF="http://java.sun.com/products/jdk/1.2/doc [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.ComponentUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#contains(javax.swing.JComponent, int, int)">contains</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChild(javax.swing.JComponent, int)">getAccessibleChild</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChildrenCount(javax.swing.JComponent)">getAccessibleChildrenCount</A>, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicAlignmentRulerUI(javax.swing.JComponent)"><!-- --></A><H3>
+BasicAlignmentRulerUI</H3>
+<PRE>
+public <B>BasicAlignmentRulerUI</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getPreferredSize(javax.swing.JComponent)"><!-- --></A><H3>
+getPreferredSize</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Dimension.html">Dimension</A> <B>getPreferredSize</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#getPreferredSize(javax.swing.JComponent)">getPreferredSize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="recalculateIfInsetsChanged()"><!-- --></A><H3>
+recalculateIfInsetsChanged</H3>
+<PRE>
+protected void <B>recalculateIfInsetsChanged</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#recalculateIfInsetsChanged()">recalculateIfInsetsChanged</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paint(java.awt.Graphics, javax.swing.JComponent)"><!-- --></A><H3>
+paint</H3>
+<PRE>
+public void <B>paint</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#paint(java.awt.Graphics, javax.swing.JComponent)">paint</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paintThumb(java.awt.Graphics)"><!-- --></A><H3>
+paintThumb</H3>
+<PRE>
+public void <B>paintThumb</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#paintThumb(java.awt.Graphics)">paintThumb</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paintTrack(java.awt.Graphics)"><!-- --></A><H3>
+paintTrack</H3>
+<PRE>
+public void <B>paintTrack</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#paintTrack(java.awt.Graphics)">paintTrack</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calculateGeometry()"><!-- --></A><H3>
+calculateGeometry</H3>
+<PRE>
+protected void <B>calculateGeometry</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateGeometry()">calculateGeometry</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calculateTrackBuffer()"><!-- --></A><H3>
+calculateTrackBuffer</H3>
+<PRE>
+protected void <B>calculateTrackBuffer</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateTrackBuffer()">calculateTrackBuffer</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calculateTrackRect()"><!-- --></A><H3>
+calculateTrackRect</H3>
+<PRE>
+protected void <B>calculateTrackRect</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateTrackRect()">calculateTrackRect</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="calculateThumbLocation()"><!-- --></A><H3>
+calculateThumbLocation</H3>
+<PRE>
+protected void <B>calculateThumbLocation</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html#calculateThumbLocation()">calculateThumbLocation</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html">BasicSliderUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createUI(javax.swing.JComponent)"><!-- --></A><H3>
+createUI</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A> <B>createUI</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentRulerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.plaf.basic.BasicSliderUI">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html
new file mode 100644
index 0000000..d97664c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html
@@ -0,0 +1,335 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+BasicAlignmentViewerUI.KeyScroller
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicAlignmentViewerUI.KeyScroller";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.KeyScroller.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class BasicAlignmentViewerUI.KeyScroller</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BasicAlignmentViewerUI.KeyScroller</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#DOWN">DOWN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#LEFT">LEFT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#RIGHT">RIGHT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#UP">UP</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#BasicAlignmentViewerUI.KeyScroller(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, int)">BasicAlignmentViewerUI.KeyScroller</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ int direction)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="UP"><!-- --></A><H3>
+UP</H3>
+<PRE>
+public static final int <B>UP</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.UP">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="DOWN"><!-- --></A><H3>
+DOWN</H3>
+<PRE>
+public static final int <B>DOWN</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.DOWN">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="RIGHT"><!-- --></A><H3>
+RIGHT</H3>
+<PRE>
+public static final int <B>RIGHT</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.RIGHT">Constant Field Values</A></DL>
+</DL>
+<HR>
+
+<A NAME="LEFT"><!-- --></A><H3>
+LEFT</H3>
+<PRE>
+public static final int <B>LEFT</B></PRE>
+<DL>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../constant-values.html#uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.KeyScroller.LEFT">Constant Field Values</A></DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicAlignmentViewerUI.KeyScroller(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer, int)"><!-- --></A><H3>
+BasicAlignmentViewerUI.KeyScroller</H3>
+<PRE>
+public <B>BasicAlignmentViewerUI.KeyScroller</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer,
+ int direction)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.KeyScroller.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html
new file mode 100644
index 0000000..1bfbdfa
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html
@@ -0,0 +1,248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+BasicAlignmentViewerUI.PointListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicAlignmentViewerUI.PointListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.PointListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class BasicAlignmentViewerUI.PointListener</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.PointListener</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BasicAlignmentViewerUI.PointListener</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html#BasicAlignmentViewerUI.PointListener()">BasicAlignmentViewerUI.PointListener</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html#stateChanged(javax.swing.event.ChangeEvent)">stateChanged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeEvent.html">ChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicAlignmentViewerUI.PointListener()"><!-- --></A><H3>
+BasicAlignmentViewerUI.PointListener</H3>
+<PRE>
+public <B>BasicAlignmentViewerUI.PointListener</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="stateChanged(javax.swing.event.ChangeEvent)"><!-- --></A><H3>
+stateChanged</H3>
+<PRE>
+public void <B>stateChanged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeEvent.html">ChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>stateChanged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.PointListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html
new file mode 100644
index 0000000..ae82f95
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html
@@ -0,0 +1,248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+BasicAlignmentViewerUI.SelectionClearer
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicAlignmentViewerUI.SelectionClearer";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.SelectionClearer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class BasicAlignmentViewerUI.SelectionClearer</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionClearer</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BasicAlignmentViewerUI.SelectionClearer</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html#BasicAlignmentViewerUI.SelectionClearer()">BasicAlignmentViewerUI.SelectionClearer</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicAlignmentViewerUI.SelectionClearer()"><!-- --></A><H3>
+BasicAlignmentViewerUI.SelectionClearer</H3>
+<PRE>
+public <B>BasicAlignmentViewerUI.SelectionClearer</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.SelectionClearer.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html
new file mode 100644
index 0000000..73de876
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html
@@ -0,0 +1,248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+BasicAlignmentViewerUI.SelectionToggler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicAlignmentViewerUI.SelectionToggler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.SelectionToggler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class BasicAlignmentViewerUI.SelectionToggler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI.SelectionToggler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BasicAlignmentViewerUI.SelectionToggler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html#BasicAlignmentViewerUI.SelectionToggler()">BasicAlignmentViewerUI.SelectionToggler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html#actionPerformed(java.awt.event.ActionEvent)">actionPerformed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicAlignmentViewerUI.SelectionToggler()"><!-- --></A><H3>
+BasicAlignmentViewerUI.SelectionToggler</H3>
+<PRE>
+public <B>BasicAlignmentViewerUI.SelectionToggler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="actionPerformed(java.awt.event.ActionEvent)"><!-- --></A><H3>
+actionPerformed</H3>
+<PRE>
+public void <B>actionPerformed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionEvent.html">ActionEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>actionPerformed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.SelectionToggler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html
new file mode 100644
index 0000000..77ff0a0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html
@@ -0,0 +1,1014 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+BasicAlignmentViewerUI
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicAlignmentViewerUI";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class BasicAlignmentViewerUI</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">javax.swing.plaf.ComponentUI</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseMotionListener.html">MouseMotionListene [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html">MetalAlignmentViewerUI</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BasicAlignmentViewerUI</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A></DL>
+
+<P>
+BasicAlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:30:36 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: BasicAlignmentViewerUI.java,v 1.28 2001/04/11 17:04:42 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html">BasicAlignmentViewerUI.PointListener</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html">BasicAlignmentViewerUI.SelectionClearer</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html">BasicAlignmentViewerUI.SelectionToggler</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#BasicAlignmentViewerUI()">BasicAlignmentViewerUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#createUI(javax.swing.JComponent)">createUI</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getCellBounds</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Rectangle)">getCellBounds</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getPointAtSequencePoint(int, int)">getPointAtSequencePoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getPointAtSequencePoint</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getSequenceAlignmentRectangleAtRectangle(java.awt.Rectangle)">getSequenceAlignmentRectangleAtRectangle</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getSequencePointAtPoint(int, int)">getSequencePointAtPoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#installKeyboardActions(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)">installKeyboardActions</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#installListeners()">installListeners</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#installUI(javax.swing.JComponent)">installUI</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseClicked(java.awt.event.MouseEvent)">mouseClicked</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseDragged(java.awt.event.MouseEvent)">mouseDragged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseEntered(java.awt.event.MouseEvent)">mouseEntered</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseExited(java.awt.event.MouseEvent)">mouseExited</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseMoved(java.awt.event.MouseEvent)">mouseMoved</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mousePressed(java.awt.event.MouseEvent)">mousePressed</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#mouseReleased(java.awt.event.MouseEvent)">mouseReleased</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paint(java.awt.Graphics, javax.swing.JComponent)">paint</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintCells(java.awt.Graphics, javax.swing.JComponent)">paintCells</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintFocusRect(java.awt.Graphics, java.awt.Rectangle)">paintFocusRect</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintImmediately(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">paintImmediately</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#paintSelection(java.awt.Graphics, javax.swing.JComponent)">paintSelection</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#propertyChange(java.beans.PropertyChangeEvent)">propertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#registerKey(int, int)">registerKey</A></B>(int keyEvent,
+ int direction)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#registerKey(java.lang.String, int)">registerKey</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyEvent,
+ int direction)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#renderCell(java.awt.Graphics, int, int, int, int, java.awt.Rectangle, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, uk.ac.man.bioinf.sequence.Element)">renderCell</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int currX,
+ int currY,
+ int cellWidth,
+ int cellHeight,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> rendererLocation,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#repaint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">repaint</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#setCursorBlink()">setCursorBlink</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#uninstallListeners()">uninstallListeners</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#uninstallUI(javax.swing.JComponent)">uninstallUI</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#unsetCursorBlink()">unsetCursorBlink</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(java.awt.Point)">getSequencePointAtPoint</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.ComponentUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#contains(javax.swing.JComponent, int, int)">contains</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChild(javax.swing.JComponent, int)">getAccessibleChild</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChildrenCount(javax.swing.JComponent)">getAccessibleChildrenCount</A>, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicAlignmentViewerUI()"><!-- --></A><H3>
+BasicAlignmentViewerUI</H3>
+<PRE>
+public <B>BasicAlignmentViewerUI</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="createUI(javax.swing.JComponent)"><!-- --></A><H3>
+createUI</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A> <B>createUI</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="installUI(javax.swing.JComponent)"><!-- --></A><H3>
+installUI</H3>
+<PRE>
+public void <B>installUI</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#installUI(javax.swing.JComponent)">installUI</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="uninstallUI(javax.swing.JComponent)"><!-- --></A><H3>
+uninstallUI</H3>
+<PRE>
+public void <B>uninstallUI</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> comp)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#uninstallUI(javax.swing.JComponent)">uninstallUI</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="installListeners()"><!-- --></A><H3>
+installListeners</H3>
+<PRE>
+public void <B>installListeners</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="uninstallListeners()"><!-- --></A><H3>
+uninstallListeners</H3>
+<PRE>
+public void <B>uninstallListeners</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paintFocusRect(java.awt.Graphics, java.awt.Rectangle)"><!-- --></A><H3>
+paintFocusRect</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>paintFocusRect</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paint(java.awt.Graphics, javax.swing.JComponent)"><!-- --></A><H3>
+paint</H3>
+<PRE>
+public void <B>paint</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#paint(java.awt.Graphics, javax.swing.JComponent)">paint</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paintCells(java.awt.Graphics, javax.swing.JComponent)"><!-- --></A><H3>
+paintCells</H3>
+<PRE>
+protected void <B>paintCells</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paintSelection(java.awt.Graphics, javax.swing.JComponent)"><!-- --></A><H3>
+paintSelection</H3>
+<PRE>
+protected void <B>paintSelection</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A> c)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="repaint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+repaint</H3>
+<PRE>
+protected void <B>repaint</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="paintImmediately(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+paintImmediately</H3>
+<PRE>
+protected void <B>paintImmediately</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="renderCell(java.awt.Graphics, int, int, int, int, java.awt.Rectangle, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+renderCell</H3>
+<PRE>
+protected void <B>renderCell</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ int currX,
+ int currY,
+ int cellWidth,
+ int cellHeight,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> rendererLocation,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAlignmentRectangleAtRectangle(java.awt.Rectangle)"><!-- --></A><H3>
+getSequenceAlignmentRectangleAtRectangle</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getSequenceAlignmentRectangleAtRectangle</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequencePointAtPoint(int, int)"><!-- --></A><H3>
+getSequencePointAtPoint</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getSequencePointAtPoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(int, int)">getSequencePointAtPoint</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPointAtSequencePoint(int, int)"><!-- --></A><H3>
+getPointAtSequencePoint</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> <B>getPointAtSequencePoint</B>(int x,
+ int y)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getPointAtSequencePoint(int, int)">getPointAtSequencePoint</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getPointAtSequencePoint</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Point.html">Point</A> <B>getPointAtSequencePoint</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getPointAtSequencePoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getPointAtSequencePoint</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+getCellBounds</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>getCellBounds</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getCellBounds</A></CODE> in class <CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, java.awt.Rectangle)"><!-- --></A><H3>
+getCellBounds</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> <B>getCellBounds</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Rectangle.html">Rectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setCursorBlink()"><!-- --></A><H3>
+setCursorBlink</H3>
+<PRE>
+public void <B>setCursorBlink</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="unsetCursorBlink()"><!-- --></A><H3>
+unsetCursorBlink</H3>
+<PRE>
+public void <B>unsetCursorBlink</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="propertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+propertyChange</H3>
+<PRE>
+public void <B>propertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> pce)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>propertyChange</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="installKeyboardActions(uk.ac.man.bioinf.gui.viewer.JAlignmentViewer)"><!-- --></A><H3>
+installKeyboardActions</H3>
+<PRE>
+protected void <B>installKeyboardActions</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.html">JAlignmentViewer</A> viewer)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="registerKey(java.lang.String, int)"><!-- --></A><H3>
+registerKey</H3>
+<PRE>
+protected void <B>registerKey</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> keyEvent,
+ int direction)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="registerKey(int, int)"><!-- --></A><H3>
+registerKey</H3>
+<PRE>
+protected void <B>registerKey</B>(int keyEvent,
+ int direction)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseClicked(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseClicked</H3>
+<PRE>
+public void <B>mouseClicked</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseClicked</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseEntered(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseEntered</H3>
+<PRE>
+public void <B>mouseEntered</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseEntered</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseExited(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseExited</H3>
+<PRE>
+public void <B>mouseExited</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseExited</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mousePressed(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mousePressed</H3>
+<PRE>
+public void <B>mousePressed</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mousePressed</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseReleased(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseReleased</H3>
+<PRE>
+public void <B>mouseReleased</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseReleased</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseDragged(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseDragged</H3>
+<PRE>
+public void <B>mouseDragged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseDragged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseMotionListener.html">MouseMotionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mouseMoved(java.awt.event.MouseEvent)"><!-- --></A><H3>
+mouseMoved</H3>
+<PRE>
+public void <B>mouseMoved</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseEvent.html">MouseEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>mouseMoved</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseMotionListener.html">MouseMotionListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicAlignmentViewerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html
new file mode 100644
index 0000000..3c2a30a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html
@@ -0,0 +1,272 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+MetalAlignmentViewerUI
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="MetalAlignmentViewerUI";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MetalAlignmentViewerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.plaf</FONT>
+<BR>
+Class MetalAlignmentViewerUI</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">javax.swing.plaf.ComponentUI</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.plaf.MetalAlignmentViewerUI</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseListener.html">MouseListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/MouseMotionListener.html">MouseMotionListene [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>MetalAlignmentViewerUI</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></DL>
+
+<P>
+MetalAlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:32:29 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: MetalAlignmentViewerUI.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html">BasicAlignmentViewerUI.KeyScroller</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html">BasicAlignmentViewerUI.PointListener</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html">BasicAlignmentViewerUI.SelectionClearer</A>, <A HREF="../../../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html#MetalAlignmentViewerUI()">MetalAlignmentViewerUI</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#createUI(javax.swing.JComponent)">createUI</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">getCellBounds</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html#getCellBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, jav [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html">AlignmentViewerUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html#getSequencePointAtPoint(java.awt.Point)">getSequencePointAtPoint</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.plaf.ComponentUI"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html">ComponentUI</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#contains(javax.swing.JComponent, int, int)">contains</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChild(javax.swing.JComponent, int)">getAccessibleChild</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html#getAccessibleChildrenCount(javax.swing.JComponent)">getAccessibleChildrenCount</A>, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MetalAlignmentViewerUI()"><!-- --></A><H3>
+MetalAlignmentViewerUI</H3>
+<PRE>
+public <B>MetalAlignmentViewerUI</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MetalAlignmentViewerUI.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI">NESTED</A> | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-frame.html
new file mode 100644
index 0000000..7088994
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-frame.html
@@ -0,0 +1,40 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.plaf()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.plaf()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.viewer.plaf</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentRulerUI.html" TARGET="classFrame">AlignmentRulerUI</A>
+<BR>
+<A HREF="AlignmentViewerUI.html" TARGET="classFrame">AlignmentViewerUI</A>
+<BR>
+<A HREF="BasicAlignmentRulerUI.html" TARGET="classFrame">BasicAlignmentRulerUI</A>
+<BR>
+<A HREF="BasicAlignmentViewerUI.html" TARGET="classFrame">BasicAlignmentViewerUI</A>
+<BR>
+<A HREF="MetalAlignmentViewerUI.html" TARGET="classFrame">MetalAlignmentViewerUI</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html
new file mode 100644
index 0000000..9a5c432
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html
@@ -0,0 +1,165 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.plaf()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.plaf()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.viewer.plaf
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentRulerUI.html">AlignmentRulerUI</A></B></TD>
+<TD>AlignmentRulerUI.java
+
+
+ Created: Thu Mar 23 17:10:05 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentViewerUI.html">AlignmentViewerUI</A></B></TD>
+<TD>AlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:29:34 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="BasicAlignmentRulerUI.html">BasicAlignmentRulerUI</A></B></TD>
+<TD>BasicAlignmentRulerUI.java
+
+
+ Created: Thu Mar 23 17:10:31 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="BasicAlignmentViewerUI.html">BasicAlignmentViewerUI</A></B></TD>
+<TD>BasicAlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:30:36 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MetalAlignmentViewerUI.html">MetalAlignmentViewerUI</A></B></TD>
+<TD>MetalAlignmentViewerUI.java
+
+
+ Created: Tue Mar 14 16:32:29 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html
new file mode 100644
index 0000000..c8a91c8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.plaf Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.plaf Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.viewer.plaf
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.KeyScroller.html"><B>BasicAlignmentViewerUI.KeyScroller</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.PointListener.html"><B>BasicAlignmentViewerUI.PointListener</B></A> (implements javax.swing.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/ChangeListener.html">ChangeListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionClearer.html"><B>BasicAlignmentViewerUI.SelectionClearer</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.SelectionToggler.html"><B>BasicAlignmentViewerUI.SelectionToggler</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ActionListener.html">ActionListener</A>)
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/ComponentUI.html"><B>ComponentUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.html"><B>AlignmentRulerUI</B></A><LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.html"><B>AlignmentViewerUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.html"><B>BasicAlignmentViewerUI</B></A> (implements javax.swing.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/event/MouseInputListener.html">MouseInputListener</A>, java.beans.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.html"><B>MetalAlignmentViewerUI</B></A></UL>
+</UL>
+<LI TYPE="circle">class javax.swing.plaf.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/SliderUI.html"><B>SliderUI</B></A><UL>
+<LI TYPE="circle">class javax.swing.plaf.basic.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/plaf/basic/BasicSliderUI.html"><B>BasicSliderUI</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.plaf.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.html"><B>BasicAlignmentRulerUI</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/event/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html
new file mode 100644
index 0000000..9b47f40
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html
@@ -0,0 +1,426 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:18 BST 2002 -->
+<TITLE>
+AlignmentViewerTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentViewerTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentViewerTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.test</FONT>
+<BR>
+Class AlignmentViewerTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">java.awt.Window</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">java.awt.Frame</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">javax.swing.JFrame</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, <A HREF="http:/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignmentViewerTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></DL>
+
+<P>
+AlignmentViewerTest.java
+
+
+ Created: Wed Mar 15 20:11:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentViewerTest.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.test.AlignmentViewerTest">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.AccessibleJFrame.html">JFrame.AccessibleJFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.AccessibleAWTFrame.html">Frame.AccessibleAWTFrame</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.AccessibleAWTWindow.html">Window.AccessibleAWTWindow</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#EXIT_ON_CLOSE">EXIT_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPane">rootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#rootPaneCheckingEnabled">rootPaneCheckingEnabled</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#CROSSHAIR_CURSOR">CROSSHAIR_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#DEFAULT_CURSOR">DEFAULT_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#E_RESIZE_CURSOR">E_RESIZE_CURSOR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#HAND_CURSOR">HAND_CURSOR</A>, <A HREF="http://java.sun.com/products/ [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.WindowConstants"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html">WindowConstants</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DISPOSE_ON_CLOSE">DISPOSE_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#DO_NOTHING_ON_CLOSE">DO_NOTHING_ON_CLOSE</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstants.html#HIDE_ON_CLOSE">HIDE_ON_CLOSE</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html#AlignmentViewerTest()">AlignmentViewerTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JFrame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html">JFrame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#createRootPane()">createRootPane</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#frameInit()">frameInit</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html#getAccessibleContext()">getAccessib [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Frame"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html">Frame</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getCursorType()">getCursorType</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html#getExtendedState()">getExtendedState</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Window"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html">Window</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html#addWindowFocusListener(java.awt.event.WindowFocusL [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.MenuContainer"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#getFont()">getFont</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html#postEvent(java.awt.Event)">postEvent</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentViewerTest()"><!-- --></A><H3>
+AlignmentViewerTest</H3>
+<PRE>
+public <B>AlignmentViewerTest</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentViewerTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JFrame">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JFrame">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html
new file mode 100644
index 0000000..8e59f82
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:19 BST 2002 -->
+<TITLE>
+BasicWindowMonitor
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="BasicWindowMonitor";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicWindowMonitor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.test</FONT>
+<BR>
+Class BasicWindowMonitor</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html">java.awt.event.WindowAdapter</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.test.BasicWindowMonitor</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowFocusListener.html">WindowFocusListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowListener.html">WindowListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowStateListener.html">WindowStateListen [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>BasicWindowMonitor</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html">WindowAdapter</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html#BasicWindowMonitor()">BasicWindowMonitor</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html#windowClosing(java.awt.event.WindowEvent)">windowClosing</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowEvent.html">WindowEvent</A> e)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.event.WindowAdapter"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html">WindowAdapter</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html#windowActivated(java.awt.event.WindowEvent)">windowActivated</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html#windowClosed(java.awt.event.WindowEvent)">windowClosed</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html#windowDeactivated(java.awt.event.WindowEvent)">windowDeactivated</A>, <A HREF="http://jav [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="BasicWindowMonitor()"><!-- --></A><H3>
+BasicWindowMonitor</H3>
+<PRE>
+public <B>BasicWindowMonitor</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="windowClosing(java.awt.event.WindowEvent)"><!-- --></A><H3>
+windowClosing</H3>
+<PRE>
+public void <B>windowClosing</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowEvent.html">WindowEvent</A> e)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>windowClosing</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowListener.html">WindowListener</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html#windowClosing(java.awt.event.WindowEvent)">windowClosing</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html">WindowAda [...]
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="BasicWindowMonitor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html
new file mode 100644
index 0000000..2abb54b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html
@@ -0,0 +1,282 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:19 BST 2002 -->
+<TITLE>
+ButtonPanelTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ButtonPanelTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ButtonPanelTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.test</FONT>
+<BR>
+Class ButtonPanelTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.test.ButtonPanelTest</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ButtonPanelTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A></DL>
+
+<P>
+ButtonPanelTest.java
+
+
+ Created: Fri May 19 17:22:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ButtonPanelTest.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html#ButtonPanelTest()">ButtonPanelTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html#itemStateChanged(java.awt.event.ItemEvent)">itemStateChanged</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemEvent.html">ItemEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ButtonPanelTest()"><!-- --></A><H3>
+ButtonPanelTest</H3>
+<PRE>
+public <B>ButtonPanelTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="itemStateChanged(java.awt.event.ItemEvent)"><!-- --></A><H3>
+itemStateChanged</H3>
+<PRE>
+public void <B>itemStateChanged</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemEvent.html">ItemEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>itemStateChanged</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ButtonPanelTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html
new file mode 100644
index 0000000..924d9cf
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html
@@ -0,0 +1,373 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:19 BST 2002 -->
+<TITLE>
+CellRendererPaneReplacement
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CellRendererPaneReplacement";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CellRendererPaneReplacement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.CellRendererPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.CellRendererPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.test</FONT>
+<BR>
+Class CellRendererPaneReplacement</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html">javax.swing.CellRendererPane</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>CellRendererPaneReplacement</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html">CellRendererPane</A></DL>
+
+<P>
+CellRendererPaneReplacement.java
+
+
+ Created: Fri Apr 14 17:02:05 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CellRendererPaneReplacement.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.test.CellRendererPaneReplacement">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.CellRendererPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html">CellRendererPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.AccessibleCellRendererPane.html">CellRendererPane.AccessibleCellRendererPane</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.CellRendererPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html">CellRendererPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html#accessibleContext">accessibleContext</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html#CellRendererPaneReplacement()">CellRendererPaneReplacement</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html#paintComponent(java.awt.Graphics, java.awt.Component, java.awt.Container, int, int, int, int, boolean)">paintComponent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> c,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A> p,
+ int x,
+ int y,
+ int w,
+ int h,
+ boolean shouldValidate)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.CellRendererPane"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html">CellRendererPane</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html#addImpl(java.awt.Component, java.lang.Object, int)">addImpl</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html#invalidate()">invalidate</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/Cel [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CellRendererPaneReplacement()"><!-- --></A><H3>
+CellRendererPaneReplacement</H3>
+<PRE>
+public <B>CellRendererPaneReplacement</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="paintComponent(java.awt.Graphics, java.awt.Component, java.awt.Container, int, int, int, int, boolean)"><!-- --></A><H3>
+paintComponent</H3>
+<PRE>
+public void <B>paintComponent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Graphics.html">Graphics</A> g,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A> c,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A> p,
+ int x,
+ int y,
+ int w,
+ int h,
+ boolean shouldValidate)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html#paintComponent(java.awt.Graphics, java.awt.Component, java.awt.Container, int, int, int, int, boolean)">paintComponent</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html">CellRendererPane</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CellRendererPaneReplacement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.CellRendererPane">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.CellRendererPane">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html
new file mode 100644
index 0000000..7a1e23f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:19 BST 2002 -->
+<TITLE>
+SingleSelectionModelTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SingleSelectionModelTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SliderExample.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleSelectionModelTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.test</FONT>
+<BR>
+Class SingleSelectionModelTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.test.SingleSelectionModelTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SingleSelectionModelTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SingleSelectionModelTest.java
+
+
+ Created: Wed Apr 12 17:34:46 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SingleSelectionModelTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html#SingleSelectionModelTest()">SingleSelectionModelTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SingleSelectionModelTest()"><!-- --></A><H3>
+SingleSelectionModelTest</H3>
+<PRE>
+public <B>SingleSelectionModelTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SliderExample.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleSelectionModelTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/SliderExample.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/SliderExample.html
new file mode 100644
index 0000000..b968a17
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/SliderExample.html
@@ -0,0 +1,365 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+SliderExample
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SliderExample";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SliderExample.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.gui.viewer.test</FONT>
+<BR>
+Class SliderExample</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">java.awt.Component</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">java.awt.Container</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">javax.swing.JComponent</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">javax.swing.JPanel</A>
+ |
+ +--<B>uk.ac.man.bioinf.gui.viewer.test.SliderExample</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SliderExample</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></DL>
+
+<P>
+<DL>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.gui.viewer.test.SliderExample">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.AccessibleJPanel.html">JPanel.AccessibleJPanel</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.AccessibleJComponent.html">JComponent.AccessibleJComponent</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.AccessibleAWTContainer.html">Container.AccessibleAWTContainer</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.AccessibleAWTComponent.html">Component.AccessibleAWTComponent</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.BltBufferStrategy.html">Component.BltBufferStrategy</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.FlipBufferStrategy.html">Component.FlipBufferStrategy</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#accessibleContext">accessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#listenerList">listenerList</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#TOOL_TIP_TEXT_KEY">TOOL_TIP_TEXT_KEY</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#ui">ui</A>, <A HREF="http://java.s [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#BOTTOM_ALIGNMENT">BOTTOM_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#CENTER_ALIGNMENT">CENTER_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#LEFT_ALIGNMENT">LEFT_ALIGNMENT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#RIGHT_ALIGNMENT">RIGHT_ALIGNMENT</A>, <A HREF="htt [...]
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.awt.image.ImageObserver"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from interface java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ABORT">ABORT</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ALLBITS">ALLBITS</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#ERROR">ERROR</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html#FRAMEBITS">FRAMEBITS</A>, <A HREF="http://java.sun.com/products/jdk/ [...]
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SliderExample.html#SliderExample()">SliderExample</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SliderExample.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] s)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JPanel"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html">JPanel</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getAccessibleContext()">getAccessibleContext</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUI()">getUI</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#getUIClassID()">getUIClassID</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html#paramString()">paramString</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_javax.swing.JComponent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html">JComponent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addAncestorListener(javax.swing.event.AncestorListener)">addAncestorListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addNotify()">addNotify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A>, <A HREF="http://java.sun.com/p [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Container"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html">Container</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, int)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html#add(java.awt.Component, java.lang.Object, [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.awt.Component"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html">Component</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#action(java.awt.Event, java.lang.Object)">action</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#add(java.awt.PopupMenu)">add</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html#addComponentListener(java.awt.event.ComponentListener)">addComponentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.h [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SliderExample()"><!-- --></A><H3>
+SliderExample</H3>
+<PRE>
+public <B>SliderExample</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] s)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SliderExample.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_javax.swing.JPanel">NESTED</A> | <A HREF="#fields_inherited_from_class_javax.swing.JComponent">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-frame.html
new file mode 100644
index 0000000..e5374f4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-frame.html
@@ -0,0 +1,42 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.gui.viewer.test</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentViewerTest.html" TARGET="classFrame">AlignmentViewerTest</A>
+<BR>
+<A HREF="BasicWindowMonitor.html" TARGET="classFrame">BasicWindowMonitor</A>
+<BR>
+<A HREF="ButtonPanelTest.html" TARGET="classFrame">ButtonPanelTest</A>
+<BR>
+<A HREF="CellRendererPaneReplacement.html" TARGET="classFrame">CellRendererPaneReplacement</A>
+<BR>
+<A HREF="SingleSelectionModelTest.html" TARGET="classFrame">SingleSelectionModelTest</A>
+<BR>
+<A HREF="SliderExample.html" TARGET="classFrame">SliderExample</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-summary.html
new file mode 100644
index 0000000..73fba11
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-summary.html
@@ -0,0 +1,166 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/io/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.gui.viewer.test
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentViewerTest.html">AlignmentViewerTest</A></B></TD>
+<TD>AlignmentViewerTest.java
+
+
+ Created: Wed Mar 15 20:11:02 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="BasicWindowMonitor.html">BasicWindowMonitor</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ButtonPanelTest.html">ButtonPanelTest</A></B></TD>
+<TD>ButtonPanelTest.java
+
+
+ Created: Fri May 19 17:22:31 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CellRendererPaneReplacement.html">CellRendererPaneReplacement</A></B></TD>
+<TD>CellRendererPaneReplacement.java
+
+
+ Created: Fri Apr 14 17:02:05 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SingleSelectionModelTest.html">SingleSelectionModelTest</A></B></TD>
+<TD>SingleSelectionModelTest.java
+
+
+ Created: Wed Apr 12 17:34:46 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SliderExample.html">SliderExample</A></B></TD>
+<TD> </TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/io/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-tree.html
new file mode 100644
index 0000000..dc1955c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/gui/viewer/test/package-tree.html
@@ -0,0 +1,159 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.gui.viewer.test Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.gui.viewer.test Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/io/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.gui.viewer.test
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.html"><B>ButtonPanelTest</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/ItemListener.html">ItemListener</A>)
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Component.html"><B>Component</B></A> (implements java.awt.image.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/image/ImageObserver.html">ImageObserver</A>, java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>, java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Container.html"><B>Container</B></A><UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/CellRendererPane.html"><B>CellRendererPane</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.html"><B>CellRendererPaneReplacement</B></A></UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JComponent.html"><B>JComponent</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JPanel.html"><B>JPanel</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SliderExample.html"><B>SliderExample</B></A></UL>
+</UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Window.html"><B>Window</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>)
+<UL>
+<LI TYPE="circle">class java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/Frame.html"><B>Frame</B></A> (implements java.awt.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/MenuContainer.html">MenuContainer</A>)
+<UL>
+<LI TYPE="circle">class javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/JFrame.html"><B>JFrame</B></A> (implements javax.accessibility.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/accessibility/Accessible.html">Accessible</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/RootPaneContainer.html">RootPaneContainer</A>, javax.swing.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/javax/swing/WindowConstan [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.html"><B>AlignmentViewerTest</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.html"><B>SingleSelectionModelTest</B></A><LI TYPE="circle">class java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowAdapter.html"><B>WindowAdapter</B></A> (implements java.awt.event.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/awt/event/WindowFocusListener.html">WindowFocusListener</A>, java [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.gui.viewer.test.<A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.html"><B>BasicWindowMonitor</B></A></UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/gui/viewer/plaf/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/io/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/AlignmentInputParser.html b/doc/javadoc/uk/ac/man/bioinf/io/AlignmentInputParser.html
new file mode 100644
index 0000000..e56dcf9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/AlignmentInputParser.html
@@ -0,0 +1,281 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+AlignmentInputParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentInputParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Interface AlignmentInputParser</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentInputParser</B></DL>
+
+<P>
+This is an interface that provides a definition for any sequence
+ parsers. It takes input and returns a sequence alignment
+ object. Parsers may <b>or</b> may not have state attached to
+ them. Furthermore they may be re-entered <b>or</b> alternatively
+ they may not. You have been warned.
+ <p>
+ One thing which cannot be enforced in the interface is that every
+ parser should have a default constructor (ie no arguments to the
+ constructor). This is because the parsers are generated through
+ Class.newInstance().
+
+
+ Created: Thu May 25 23:01:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentInputParser.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ Returns the description of this alignment parser, and should be
+ human readable/understandable.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ This method returns a sequence alignment from a buffered reader
+ input stream.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>parse</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>parse</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD>This method returns a sequence alignment from a buffered reader
+ input stream.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>reader</CODE> - the input stream<DD><CODE>eh</CODE> - exception handler
+<DT><B>Returns:</B><DD>the sequence alignment
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDescription</B>()</PRE>
+<DL>
+<DD>Returns the description of this alignment parser, and should be
+ human readable/understandable.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the description</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/AlignmentOutputParser.html b/doc/javadoc/uk/ac/man/bioinf/io/AlignmentOutputParser.html
new file mode 100644
index 0000000..e44f630
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/AlignmentOutputParser.html
@@ -0,0 +1,257 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+AlignmentOutputParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentOutputParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentOutputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Interface AlignmentOutputParser</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html">MotProteinParser</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentOutputParser</B></DL>
+
+<P>
+This is an interface that provides a definition for any sequence
+ output parsing. It takes a sequence alignment and returns a
+ writer. Parsers may <b>or</b> may not have state attached to them,
+ and furthermore, they may be re-entered <b>or</b> alternately they
+ may not. You have been warned!
+ <p>
+ One thing that cannot be enforced in the interface is, every parser
+ should have a default constructor (i.e., no arguments to the
+ constructor). This is because the parsers are generated through
+ Class.newInstance().
+
+
+ Created: Mon Jul 31 13:04:06 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentOutputParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ Returns the description of this alignment output parser, and
+ should be human readable/understandable.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)">write</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> writer,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ Returns a writer for output, when provided with a sequence
+ alignment.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+write</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> <B>write</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> writer,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</PRE>
+<DL>
+<DD>Returns a writer for output, when provided with a sequence
+ alignment. Exceptions are handled by the supplied exception
+ handler.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>eh</CODE> - the exception handler
+<DT><B>Returns:</B><DD>the writer for output</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDescription</B>()</PRE>
+<DL>
+<DD>Returns the description of this alignment output parser, and
+ should be human readable/understandable.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the description</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentOutputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html
new file mode 100644
index 0000000..a477249
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html
@@ -0,0 +1,261 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+DefaultParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class DefaultParserExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.DefaultParserExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultParserExceptionHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DL>
+
+<P>
+This parser exception handler does very little.
+
+
+ Created: Sat Jun 3 18:14:01 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultParserExceptionHandler.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html#DefaultParserExceptionHandler()">DefaultParserExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</CODE>
+
+<BR>
+ Handles exceptions thrown by a sequence parser.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultParserExceptionHandler()"><!-- --></A><H3>
+DefaultParserExceptionHandler</H3>
+<PRE>
+public <B>DefaultParserExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+handleException</H3>
+<PRE>
+public void <B>handleException</B>(<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></B></DD>
+<DD>Handles exceptions thrown by a sequence parser.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the exception</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html b/doc/javadoc/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html
new file mode 100644
index 0000000..c502d3a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html
@@ -0,0 +1,329 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+InvalidSequenceTypeParserException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvalidSequenceTypeParserException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvalidSequenceTypeParserException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class InvalidSequenceTypeParserException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">uk.ac.man.bioinf.io.ParserException</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.InvalidSequenceTypeParserException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>InvalidSequenceTypeParserException</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A></DL>
+
+<P>
+This exception is cast when there is a mismatch of sequence types
+ when dealing with parsers.
+
+
+ Created: Tue Aug 8 12:32:18 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InvalidSequenceTypeParserException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.io.InvalidSequenceTypeParserException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException()">InvalidSequenceTypeParserException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException(uk.ac.man.bioinf.sequence.SequenceType)">InvalidSequenceTypeParserException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> st)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException(java.lang.String)">InvalidSequenceTypeParserException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#InvalidSequenceTypeParserException(java.lang.String, uk.ac.man.bioinf.sequence.SequenceType)">InvalidSequenceTypeParserException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> st)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html#getExpcetedSequenceType()">getExpcetedSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the expected sequence type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getIdentifier()">getIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getPosition()">getPosition</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getSequence()">getSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvalidSequenceTypeParserException()"><!-- --></A><H3>
+InvalidSequenceTypeParserException</H3>
+<PRE>
+public <B>InvalidSequenceTypeParserException</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="InvalidSequenceTypeParserException(java.lang.String)"><!-- --></A><H3>
+InvalidSequenceTypeParserException</H3>
+<PRE>
+public <B>InvalidSequenceTypeParserException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="InvalidSequenceTypeParserException(uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+InvalidSequenceTypeParserException</H3>
+<PRE>
+public <B>InvalidSequenceTypeParserException</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> st)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="InvalidSequenceTypeParserException(java.lang.String, uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+InvalidSequenceTypeParserException</H3>
+<PRE>
+public <B>InvalidSequenceTypeParserException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> st)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getExpcetedSequenceType()"><!-- --></A><H3>
+getExpcetedSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getExpcetedSequenceType</B>()</PRE>
+<DL>
+<DD>Returns the expected sequence type.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvalidSequenceTypeParserException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/NarrowedInputStream.html b/doc/javadoc/uk/ac/man/bioinf/io/NarrowedInputStream.html
new file mode 100644
index 0000000..237c88a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/NarrowedInputStream.html
@@ -0,0 +1,302 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+NarrowedInputStream
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NarrowedInputStream";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NarrowedInputStream.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class NarrowedInputStream</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">java.io.InputStream</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.NarrowedInputStream</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>NarrowedInputStream</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></DL>
+
+<P>
+NarrowedInputStream.java
+
+ This InputStream wraps another and puts a limits access to that
+ stream. It hides all of the input that occur before the first
+ occurrence of a given input, and ends after the occurrence of the
+ second.
+
+ It may well be useful in a number of circumstances, but it should
+ be particularly good for pulling out data from the middle of an
+ HTML page between two tags.
+
+ Created: Thu Feb 8 17:39:21 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NarrowedInputStream.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html#NarrowedInputStream(java.io.InputStream, byte[], byte[])">NarrowedInputStream</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> stream,
+ byte[] start,
+ byte[] stop)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html#mark(int)">mark</A></B>(int readlimit)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html#read()">read</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.io.InputStream"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html#available()">available</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html#close()">close</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html#markSupported()">markSupported</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html#read(byte[])">read</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NarrowedInputStream(java.io.InputStream, byte[], byte[])"><!-- --></A><H3>
+NarrowedInputStream</H3>
+<PRE>
+public <B>NarrowedInputStream</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A> stream,
+ byte[] start,
+ byte[] stop)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="read()"><!-- --></A><H3>
+read</H3>
+<PRE>
+public int <B>read</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html#read()">read</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="mark(int)"><!-- --></A><H3>
+mark</H3>
+<PRE>
+public void <B>mark</B>(int readlimit)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html#mark(int)">mark</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html">InputStream</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NarrowedInputStream.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/NullParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/io/NullParserExceptionHandler.html
new file mode 100644
index 0000000..7eeac3c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/NullParserExceptionHandler.html
@@ -0,0 +1,290 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+NullParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NullParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class NullParserExceptionHandler</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.NullParserExceptionHandler</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NullParserExceptionHandler</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></DL>
+
+<P>
+NullParserExceptionHandler.java
+
+ An exception handler for all seasons
+
+ Created: Thu Feb 8 21:24:57 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NullParserExceptionHandler.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html#NullParserExceptionHandler()">NullParserExceptionHandler</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html#NullParserExceptionHandler(boolean)">NullParserExceptionHandler</A></B>(boolean dumpStack)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html#NullParserExceptionHandler(java.io.PrintWriter)">NullParserExceptionHandler</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/PrintWriter.html">PrintWriter</A> stream)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> exp)</CODE>
+
+<BR>
+ Handles exceptions thrown by a sequence parser.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NullParserExceptionHandler()"><!-- --></A><H3>
+NullParserExceptionHandler</H3>
+<PRE>
+public <B>NullParserExceptionHandler</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NullParserExceptionHandler(boolean)"><!-- --></A><H3>
+NullParserExceptionHandler</H3>
+<PRE>
+public <B>NullParserExceptionHandler</B>(boolean dumpStack)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NullParserExceptionHandler(java.io.PrintWriter)"><!-- --></A><H3>
+NullParserExceptionHandler</H3>
+<PRE>
+public <B>NullParserExceptionHandler</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/PrintWriter.html">PrintWriter</A> stream)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+handleException</H3>
+<PRE>
+public void <B>handleException</B>(<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> exp)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></B></DD>
+<DD>Handles exceptions thrown by a sequence parser.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>exp</CODE> - the exception</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/ParserException.html b/doc/javadoc/uk/ac/man/bioinf/io/ParserException.html
new file mode 100644
index 0000000..a4c8fe6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/ParserException.html
@@ -0,0 +1,390 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+ParserException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ParserException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ParserException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class ParserException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.ParserException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html">SequenceWriterException</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ParserException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+A general exception thrown up when parsing a sequence. The concept
+ is to make this more specific by sub-classing this exception.
+
+
+ Created: Tue Jun 6 18:09:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ParserException.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.io.ParserException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#ParserException(int)">ParserException</A></B>(int i)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#ParserException(int, java.lang.String)">ParserException</A></B>(int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#ParserException(java.lang.String, int)">ParserException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#ParserException(java.lang.String, int, java.lang.String)">ParserException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#ParserException(java.lang.String, int, java.lang.String, uk.ac.man.bioinf.sequence.identifier.Identifier)">ParserException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getPosition()">getPosition</A></B>()</CODE>
+
+<BR>
+ Returns the integer position in the sequence that caused the
+ exception.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getSequence()">getSequence</A></B>()</CODE>
+
+<BR>
+ Returns the sequence that caused the exception.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ParserException(int)"><!-- --></A><H3>
+ParserException</H3>
+<PRE>
+public <B>ParserException</B>(int i)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ParserException(java.lang.String, int)"><!-- --></A><H3>
+ParserException</H3>
+<PRE>
+public <B>ParserException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ParserException(int, java.lang.String)"><!-- --></A><H3>
+ParserException</H3>
+<PRE>
+public <B>ParserException</B>(int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ParserException(java.lang.String, int, java.lang.String)"><!-- --></A><H3>
+ParserException</H3>
+<PRE>
+public <B>ParserException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ParserException(java.lang.String, int, java.lang.String, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+ParserException</H3>
+<PRE>
+public <B>ParserException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getPosition()"><!-- --></A><H3>
+getPosition</H3>
+<PRE>
+public int <B>getPosition</B>()</PRE>
+<DL>
+<DD>Returns the integer position in the sequence that caused the
+ exception.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the location</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequence()"><!-- --></A><H3>
+getSequence</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getSequence</B>()</PRE>
+<DL>
+<DD>Returns the sequence that caused the exception.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ParserException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/ParserExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/io/ParserExceptionHandler.html
new file mode 100644
index 0000000..e3a9188
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/ParserExceptionHandler.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+ParserExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ParserExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Interface ParserExceptionHandler</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.html">AbstractSequenceInputParserExceptionHandler</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.html">AbstractSequenceParserExceptionHandler</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html">DefaultParserExceptionHandler</A>, <A HREF="../../../../../uk/ac/ [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ParserExceptionHandler</B></DL>
+
+<P>
+Handles exceptions generated by any sequence parsers.
+
+
+ Created: Sat Jun 3 18:07:14 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ParserExceptionHandler.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html#handleException(uk.ac.man.bioinf.io.ParserException)">handleException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</CODE>
+
+<BR>
+ Handles exceptions thrown by a sequence parser.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleException(uk.ac.man.bioinf.io.ParserException)"><!-- --></A><H3>
+handleException</H3>
+<PRE>
+public void <B>handleException</B>(<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A> e)</PRE>
+<DL>
+<DD>Handles exceptions thrown by a sequence parser.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>e</CODE> - the exception</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ParserExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/SequenceInputParser.html b/doc/javadoc/uk/ac/man/bioinf/io/SequenceInputParser.html
new file mode 100644
index 0000000..0a38659
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/SequenceInputParser.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:20 BST 2002 -->
+<TITLE>
+SequenceInputParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceInputParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Interface SequenceInputParser</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceInputParser</B></DL>
+
+<P>
+SequenceInputParser.java
+
+ This class defines the basic interface for parsing sequence files.
+
+ Created: Wed Feb 7 15:00:38 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceInputParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>parse</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDescription</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/SequenceWriterException.html b/doc/javadoc/uk/ac/man/bioinf/io/SequenceWriterException.html
new file mode 100644
index 0000000..cd20ed0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/SequenceWriterException.html
@@ -0,0 +1,250 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+SequenceWriterException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceWriterException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceWriterException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class SequenceWriterException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">uk.ac.man.bioinf.io.ParserException</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.SequenceWriterException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceWriterException</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A></DL>
+
+<P>
+An exception cast when an IOException is thrown in writing the
+ sequence out from CINEMA.
+
+
+ Created: Tue Aug 8 18:26:21 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceWriterException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.io.SequenceWriterException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html#SequenceWriterException()">SequenceWriterException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getIdentifier()">getIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getPosition()">getPosition</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getSequence()">getSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceWriterException()"><!-- --></A><H3>
+SequenceWriterException</H3>
+<PRE>
+public <B>SequenceWriterException</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceWriterException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/UnknownElementException.html b/doc/javadoc/uk/ac/man/bioinf/io/UnknownElementException.html
new file mode 100644
index 0000000..dd66724
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/UnknownElementException.html
@@ -0,0 +1,319 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+UnknownElementException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="UnknownElementException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="UnknownElementException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io</FONT>
+<BR>
+Class UnknownElementException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">uk.ac.man.bioinf.io.ParserException</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.UnknownElementException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>UnknownElementException</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A></DL>
+
+<P>
+An exception to flag an unrecognised element in a string.
+
+
+ Created: Wed Jun 7 13:28:11 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: UnknownElementException.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.io.UnknownElementException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(int)">UnknownElementException</A></B>(int i)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(int, java.lang.String)">UnknownElementException</A></B>(int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(java.lang.String, int)">UnknownElementException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(java.lang.String, int, java.lang.String)">UnknownElementException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html#UnknownElementException(java.lang.String, int, java.lang.String, uk.ac.man.bioinf.sequence.identifier.Identifier)">UnknownElementException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> seqIdent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html">ParserException</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getIdentifier()">getIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getPosition()">getPosition</A>, <A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html#getSequence()">getSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="UnknownElementException(int)"><!-- --></A><H3>
+UnknownElementException</H3>
+<PRE>
+public <B>UnknownElementException</B>(int i)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="UnknownElementException(java.lang.String, int)"><!-- --></A><H3>
+UnknownElementException</H3>
+<PRE>
+public <B>UnknownElementException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="UnknownElementException(int, java.lang.String)"><!-- --></A><H3>
+UnknownElementException</H3>
+<PRE>
+public <B>UnknownElementException</B>(int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="UnknownElementException(java.lang.String, int, java.lang.String)"><!-- --></A><H3>
+UnknownElementException</H3>
+<PRE>
+public <B>UnknownElementException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="UnknownElementException(java.lang.String, int, java.lang.String, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+UnknownElementException</H3>
+<PRE>
+public <B>UnknownElementException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ int i,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> seqIdent)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="UnknownElementException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.io.ParserException">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/io/package-frame.html
new file mode 100644
index 0000000..d3b8acc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/package-frame.html
@@ -0,0 +1,70 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../uk/ac/man/bioinf/io/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.io</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentInputParser.html" TARGET="classFrame"><I>AlignmentInputParser</I></A>
+<BR>
+<A HREF="AlignmentOutputParser.html" TARGET="classFrame"><I>AlignmentOutputParser</I></A>
+<BR>
+<A HREF="ParserExceptionHandler.html" TARGET="classFrame"><I>ParserExceptionHandler</I></A>
+<BR>
+<A HREF="SequenceInputParser.html" TARGET="classFrame"><I>SequenceInputParser</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="DefaultParserExceptionHandler.html" TARGET="classFrame">DefaultParserExceptionHandler</A>
+<BR>
+<A HREF="NarrowedInputStream.html" TARGET="classFrame">NarrowedInputStream</A>
+<BR>
+<A HREF="NullParserExceptionHandler.html" TARGET="classFrame">NullParserExceptionHandler</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="InvalidSequenceTypeParserException.html" TARGET="classFrame">InvalidSequenceTypeParserException</A>
+<BR>
+<A HREF="ParserException.html" TARGET="classFrame">ParserException</A>
+<BR>
+<A HREF="SequenceWriterException.html" TARGET="classFrame">SequenceWriterException</A>
+<BR>
+<A HREF="UnknownElementException.html" TARGET="classFrame">UnknownElementException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/io/package-summary.html
new file mode 100644
index 0000000..0e6435a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/package-summary.html
@@ -0,0 +1,207 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/viewer/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/parsers/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.io
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentInputParser.html"><I>AlignmentInputParser</I></A></B></TD>
+<TD>This is an interface that provides a definition for any sequence
+ parsers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentOutputParser.html"><I>AlignmentOutputParser</I></A></B></TD>
+<TD>This is an interface that provides a definition for any sequence
+ output parsing.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ParserExceptionHandler.html"><I>ParserExceptionHandler</I></A></B></TD>
+<TD>Handles exceptions generated by any sequence parsers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceInputParser.html"><I>SequenceInputParser</I></A></B></TD>
+<TD>SequenceInputParser.java
+
+ This class defines the basic interface for parsing sequence files.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultParserExceptionHandler.html">DefaultParserExceptionHandler</A></B></TD>
+<TD>This parser exception handler does very little.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NarrowedInputStream.html">NarrowedInputStream</A></B></TD>
+<TD>NarrowedInputStream.java
+
+ This InputStream wraps another and puts a limits access to that
+ stream.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NullParserExceptionHandler.html">NullParserExceptionHandler</A></B></TD>
+<TD>NullParserExceptionHandler.java
+
+ An exception handler for all seasons
+
+ Created: Thu Feb 8 21:24:57 2001</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvalidSequenceTypeParserException.html">InvalidSequenceTypeParserException</A></B></TD>
+<TD>This exception is cast when there is a mismatch of sequence types
+ when dealing with parsers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ParserException.html">ParserException</A></B></TD>
+<TD>A general exception thrown up when parsing a sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceWriterException.html">SequenceWriterException</A></B></TD>
+<TD>An exception cast when an IOException is thrown in writing the
+ sequence out from CINEMA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="UnknownElementException.html">UnknownElementException</A></B></TD>
+<TD>An exception to flag an unrecognised element in a string.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/viewer/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/parsers/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/io/package-tree.html
new file mode 100644
index 0000000..4060b99
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/package-tree.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/viewer/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/parsers/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.io
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/DefaultParserExceptionHandler.html"><B>DefaultParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<LI TYPE="circle">class java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/InputStream.html"><B>InputStream</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/NarrowedInputStream.html"><B>NarrowedInputStream</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/NullParserExceptionHandler.html"><B>NullParserExceptionHandler</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A>)
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserException.html"><B>ParserException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.html"><B>InvalidSequenceTypeParserException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/SequenceWriterException.html"><B>SequenceWriterException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/UnknownElementException.html"><B>UnknownElementException</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html"><B>AlignmentInputParser</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html"><B>AlignmentOutputParser</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.io.<A HREF="../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html"><B>ParserExceptionHandler</B></A><LI TYPE="circle">interface uk.ac.ma [...]
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/gui/viewer/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/io/parsers/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html
new file mode 100644
index 0000000..1e9aad4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+AbstractProteinAlignmentInputParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractProteinAlignmentInputParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractProteinAlignmentInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.parsers</FONT>
+<BR>
+Class AbstractProteinAlignmentInputParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractProteinAlignmentInputParser</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A></DL>
+
+<P>
+Provides a function to parse amino acids from the input stream.
+
+
+ Created: Fri May 26 12:32:09 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractProteinAlignmentInputParser.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html#AbstractProteinAlignmentInputParser()">AbstractProteinAlignmentInputParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html#toSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">toSequence</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> description,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.AlignmentInputParser"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.io.<A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#getDescription()">getDescription</A>, <A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A>, <A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractProteinAlignmentInputParser()"><!-- --></A><H3>
+AbstractProteinAlignmentInputParser</H3>
+<PRE>
+public <B>AbstractProteinAlignmentInputParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+toSequence</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>toSequence</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> description,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractProteinAlignmentInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html
new file mode 100644
index 0000000..90eb071
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html
@@ -0,0 +1,323 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+AbstractProteinSequenceInputParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractProteinSequenceInputParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractProteinSequenceInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.parsers</FONT>
+<BR>
+Class AbstractProteinSequenceInputParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html">FastaSequenceParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractProteinSequenceInputParser</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A></DL>
+
+<P>
+AbstractProteinSequenceInputParser.java
+
+ Provides a root class for all protein sequence parsers.
+
+ Created: Wed Feb 7 15:08:25 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractProteinSequenceInputParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#AbstractProteinSequenceInputParser()">AbstractProteinSequenceInputParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#createException(int, char)">createException</A></B>(int position,
+ char elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#toElements(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">toElements</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#toSequence(uk.ac.man.bioinf.sequence.identifier.Identifier, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">toSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.SequenceInputParser"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.io.<A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html#getDescription()">getDescription</A>, <A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractProteinSequenceInputParser()"><!-- --></A><H3>
+AbstractProteinSequenceInputParser</H3>
+<PRE>
+public <B>AbstractProteinSequenceInputParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toSequence(uk.ac.man.bioinf.sequence.identifier.Identifier, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+toSequence</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>toSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toElements(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+toElements</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>toElements</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> seq,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createException(int, char)"><!-- --></A><H3>
+createException</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/io/UnknownElementException.html">UnknownElementException</A> <B>createException</B>(int position,
+ char elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractProteinSequenceInputParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html
new file mode 100644
index 0000000..5150d46
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html
@@ -0,0 +1,314 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+FastaSequenceParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FastaSequenceParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FastaSequenceParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.parsers</FONT>
+<BR>
+Class FastaSequenceParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.parsers.FastaSequenceParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FastaSequenceParser</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A></DL>
+
+<P>
+FastaSequenceParser.java
+
+
+ Created: Wed Feb 7 15:07:45 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FastaSequenceParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#FastaSequenceParser()">FastaSequenceParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.parsers.AbstractProteinSequenceInputParser"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#createException(int, char)">createException</A>, <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#toElements(java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">toElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html#toSequence(uk.ac.man.bioinf.sequence.identifier.Identifier [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FastaSequenceParser()"><!-- --></A><H3>
+FastaSequenceParser</H3>
+<PRE>
+public <B>FastaSequenceParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>parse</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>parse</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> exh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDescription</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FastaSequenceParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/MotProteinParser.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/MotProteinParser.html
new file mode 100644
index 0000000..290ca19
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/MotProteinParser.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+MotProteinParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="MotProteinParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MotProteinParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.parsers</FONT>
+<BR>
+Class MotProteinParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.parsers.MotProteinParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>MotProteinParser</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></DL>
+
+<P>
+MotProteinParser.java
+
+ Mot files are used by several of the applications that are used to
+ produce PRINTS. Its a very simple format. One line per sequence
+ (motif files tend to be fairly short alignments). Comments are
+ designated with a #. PRINTS motif's can't contain gaps so by
+ definition here this parser does not like gaps and will not write
+ them out.
+
+ Created: Mon Jan 22 16:44:15 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: MotProteinParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html#MotProteinParser()">MotProteinParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ Returns the description of this alignment output parser, and
+ should be human readable/understandable.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)">write</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> writer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ Returns a writer for output, when provided with a sequence
+ alignment.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MotProteinParser()"><!-- --></A><H3>
+MotProteinParser</H3>
+<PRE>
+public <B>MotProteinParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+write</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> <B>write</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> writer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></B></DD>
+<DD>Returns a writer for output, when provided with a sequence
+ alignment. Exceptions are handled by the supplied exception
+ handler.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)">write</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment<DD><CODE>eh</CODE> - the exception handler
+<DT><B>Returns:</B><DD>the writer for output</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDescription</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></B></DD>
+<DD>Returns the description of this alignment output parser, and
+ should be human readable/understandable.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html#getDescription()">getDescription</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the description</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MotProteinParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html
new file mode 100644
index 0000000..9e1400c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html
@@ -0,0 +1,372 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+PIRProteinAlignmentParser
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PIRProteinAlignmentParser";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PIRProteinAlignmentParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.parsers</FONT>
+<BR>
+Class PIRProteinAlignmentParser</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>, <A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>PIRProteinAlignmentParser</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></DL>
+
+<P>
+A filter that reads an alignment in PIR/NBRF protein sequence
+ format and returns a sequence alignment object. This parser has no
+ state attached to it, and may be re-entered (ie it is thread safe).
+
+
+ Created: Fri May 26 10:18:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: PIRProteinAlignmentParser.java,v 1.15 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#PIRProteinAlignmentParser()">PIRProteinAlignmentParser</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#getDescription()">getDescription</A></B>()</CODE>
+
+<BR>
+ Returns that this is a PIR/NBRF protein sequence parser.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> r,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> r,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ This function parses an input reader which contains a (set of)
+ PIR/NBRF sequence(s), and returns an alignment containing
+ them.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)">write</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> writer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</CODE>
+
+<BR>
+ This method parses a sequence alignment and writes it out to the
+ supplied writer.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.io.parsers.AbstractProteinAlignmentInputParser"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html#toSequence(java.lang.String, java.lang.String, uk.ac.man.bioinf.io.ParserExceptionHandler)">toSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PIRProteinAlignmentParser()"><!-- --></A><H3>
+PIRProteinAlignmentParser</H3>
+<PRE>
+public <B>PIRProteinAlignmentParser</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>parse</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> r,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD>This function parses an input reader which contains a (set of)
+ PIR/NBRF sequence(s), and returns an alignment containing
+ them. It only reads the protein version of PIR/NBRF format. Any
+ exceptions thrown up (except the IOException) are packaged up and
+ sent to an exception handler.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>r</CODE> - the input reader<DD><CODE>eh</CODE> - the exception handler
+<DT><B>Returns:</B><DD>the sequence alignment
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE> - if there is an error in the reader</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+parse</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>parse</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> r,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html#parse(uk.ac.man.bioinf.sequence.identifier.Identifier, java.io.Reader, uk.ac.man.bioinf.io.ParserExceptionHandler)">parse</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)"><!-- --></A><H3>
+write</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> <B>write</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> sa,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Writer.html">Writer</A> writer,
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/ParserExceptionHandler.html">ParserExceptionHandler</A> eh)</PRE>
+<DL>
+<DD>This method parses a sequence alignment and writes it out to the
+ supplied writer. It formats the output to 80 characters wide.
+ <p>
+ <b>N.B.</b>, this method does nothing with the writer other than
+ write output to it - <i>i.e.</i> it does not close the writer.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html#write(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, java.io.Writer, uk.ac.man.bioinf.io.ParserExceptionHandler)">write</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sa</CODE> - the sequence alignment to be written.<DD><CODE>writer</CODE> - the writer to which the sequence is to be written<DD><CODE>eh</CODE> - the exception handler to which exceptions are parsed.
+<DT><B>Returns:</B><DD>the writer for output</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDescription</B>()</PRE>
+<DL>
+<DD>Returns that this is a PIR/NBRF protein sequence parser.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html#getDescription()">getDescription</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the description of this parser</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PIRProteinAlignmentParser.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-frame.html
new file mode 100644
index 0000000..ab56888
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-frame.html
@@ -0,0 +1,40 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io.parsers()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io.parsers()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.io.parsers</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractProteinAlignmentInputParser.html" TARGET="classFrame">AbstractProteinAlignmentInputParser</A>
+<BR>
+<A HREF="AbstractProteinSequenceInputParser.html" TARGET="classFrame">AbstractProteinSequenceInputParser</A>
+<BR>
+<A HREF="FastaSequenceParser.html" TARGET="classFrame">FastaSequenceParser</A>
+<BR>
+<A HREF="MotProteinParser.html" TARGET="classFrame">MotProteinParser</A>
+<BR>
+<A HREF="PIRProteinAlignmentParser.html" TARGET="classFrame">PIRProteinAlignmentParser</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-summary.html
new file mode 100644
index 0000000..041d8a5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-summary.html
@@ -0,0 +1,159 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io.parsers()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io.parsers()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.io.parsers
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractProteinAlignmentInputParser.html">AbstractProteinAlignmentInputParser</A></B></TD>
+<TD>Provides a function to parse amino acids from the input stream.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractProteinSequenceInputParser.html">AbstractProteinSequenceInputParser</A></B></TD>
+<TD>AbstractProteinSequenceInputParser.java
+
+ Provides a root class for all protein sequence parsers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FastaSequenceParser.html">FastaSequenceParser</A></B></TD>
+<TD>FastaSequenceParser.java
+
+
+ Created: Wed Feb 7 15:07:45 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MotProteinParser.html">MotProteinParser</A></B></TD>
+<TD>MotProteinParser.java
+
+ Mot files are used by several of the applications that are used to
+ produce PRINTS.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PIRProteinAlignmentParser.html">PIRProteinAlignmentParser</A></B></TD>
+<TD>A filter that reads an alignment in PIR/NBRF protein sequence
+ format and returns a sequence alignment object.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-tree.html
new file mode 100644
index 0000000..bfec8e3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/parsers/package-tree.html
@@ -0,0 +1,140 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io.parsers Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io.parsers Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.io.parsers
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.html"><B>AbstractProteinAlignmentInputParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentInputParser.html">AlignmentInputParser</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.html"><B>PIRProteinAlignmentParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.html"><B>AbstractProteinSequenceInputParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../../uk/ac/man/bioinf/io/SequenceInputParser.html">SequenceInputParser</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/FastaSequenceParser.html"><B>FastaSequenceParser</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.parsers.<A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/MotProteinParser.html"><B>MotProteinParser</B></A> (implements uk.ac.man.bioinf.io.<A HREF="../../../../../../uk/ac/man/bioinf/io/AlignmentOutputParser.html">AlignmentOutputParser</A>)
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html b/doc/javadoc/uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html
new file mode 100644
index 0000000..a801e5e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+AlignmentParserIOTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentParserIOTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentParserIOTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.test</FONT>
+<BR>
+Class AlignmentParserIOTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.test.AlignmentParserIOTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignmentParserIOTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AlignmentParserIOTest.java
+
+
+ Created: Mon Aug 14 16:46:12 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentParserIOTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html#AlignmentParserIOTest()">AlignmentParserIOTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentParserIOTest()"><!-- --></A><H3>
+AlignmentParserIOTest</H3>
+<PRE>
+public <B>AlignmentParserIOTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentParserIOTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html b/doc/javadoc/uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html
new file mode 100644
index 0000000..742ca95
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+AlignmentParserInputTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentParserInputTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentParserInputTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.io.test</FONT>
+<BR>
+Class AlignmentParserInputTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.io.test.AlignmentParserInputTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignmentParserInputTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AlignmentParserInputTest.java
+
+
+ Created: Wed Jun 7 19:18:07 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentParserInputTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html#AlignmentParserInputTest()">AlignmentParserInputTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentParserInputTest()"><!-- --></A><H3>
+AlignmentParserInputTest</H3>
+<PRE>
+public <B>AlignmentParserInputTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentParserInputTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/test/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/io/test/package-frame.html
new file mode 100644
index 0000000..d46245f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/test/package-frame.html
@@ -0,0 +1,34 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/io/test/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.io.test</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentParserInputTest.html" TARGET="classFrame">AlignmentParserInputTest</A>
+<BR>
+<A HREF="AlignmentParserIOTest.html" TARGET="classFrame">AlignmentParserIOTest</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/test/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/io/test/package-summary.html
new file mode 100644
index 0000000..6c03ce7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/test/package-summary.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/module/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.io.test
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentParserInputTest.html">AlignmentParserInputTest</A></B></TD>
+<TD>AlignmentParserInputTest.java
+
+
+ Created: Wed Jun 7 19:18:07 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentParserIOTest.html">AlignmentParserIOTest</A></B></TD>
+<TD>AlignmentParserIOTest.java
+
+
+ Created: Mon Aug 14 16:46:12 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/module/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/io/test/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/io/test/package-tree.html
new file mode 100644
index 0000000..62283ab
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/io/test/package-tree.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.io.test Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.io.test Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/module/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.io.test
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.io.test.<A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserInputTest.html"><B>AlignmentParserInputTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.io.test.<A HREF="../../../../../../uk/ac/man/bioinf/io/test/AlignmentParserIOTest.html"><B>AlignmentParserIOTest</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/io/parsers/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/module/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html
new file mode 100644
index 0000000..659bcdc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html
@@ -0,0 +1,424 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+AbstractEnumeratedModuleIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractEnumeratedModuleIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeratedModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class AbstractEnumeratedModuleIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.html">CinemaBootIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.html">CinemaColorIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.html">CinemaCommandLineParserIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.html">Ci [...]
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractEnumeratedModuleIdentifier</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DL>
+
+<P>
+AbstractEnumeratedModuleIdentifier.java
+
+
+ Created: Sun May 7 17:42:13 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractEnumeratedModuleIdentifier.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#AbstractEnumeratedModuleIdentifier(java.lang.String, java.lang.String)">AbstractEnumeratedModuleIdentifier</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#AbstractEnumeratedModuleIdentifier(java.lang.String, java.lang.String, boolean)">AbstractEnumeratedModuleIdentifier</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString,
+ boolean isInterface)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getAllIdentifiers(java.lang.Class)">getAllIdentifiers</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getClassName()">getClassName</A></B>()</CODE>
+
+<BR>
+ Returns the string of the class name.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#getModuleName()">getModuleName</A></B>()</CODE>
+
+<BR>
+ Returns the name of the module being defined.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#isInterface()">isInterface</A></B>()</CODE>
+
+<BR>
+ Returns whether this module is an interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractEnumeratedModuleIdentifier(java.lang.String, java.lang.String)"><!-- --></A><H3>
+AbstractEnumeratedModuleIdentifier</H3>
+<PRE>
+public <B>AbstractEnumeratedModuleIdentifier</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AbstractEnumeratedModuleIdentifier(java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>
+AbstractEnumeratedModuleIdentifier</H3>
+<PRE>
+public <B>AbstractEnumeratedModuleIdentifier</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString,
+ boolean isInterface)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAllIdentifiers(java.lang.Class)"><!-- --></A><H3>
+getAllIdentifiers</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] <B>getAllIdentifiers</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModuleName()"><!-- --></A><H3>
+getModuleName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getModuleName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></B></DD>
+<DD>Returns the name of the module being defined.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#getModuleName()">getModuleName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getClassName()"><!-- --></A><H3>
+getClassName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getClassName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></B></DD>
+<DD>Returns the string of the class name.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#getClassName()">getClassName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the class name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isInterface()"><!-- --></A><H3>
+isInterface</H3>
+<PRE>
+public boolean <B>isInterface</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></B></DD>
+<DD>Returns whether this module is an interface.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#isInterface()">isInterface</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>whether this module is an interface.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeratedModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/DefaultModuleContext.html b/doc/javadoc/uk/ac/man/bioinf/module/DefaultModuleContext.html
new file mode 100644
index 0000000..6ba7458
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/DefaultModuleContext.html
@@ -0,0 +1,298 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:22 BST 2002 -->
+<TITLE>
+DefaultModuleContext
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultModuleContext";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultModuleContext.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class DefaultModuleContext</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">uk.ac.man.bioinf.module.ModuleContext</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.DefaultModuleContext</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>DefaultModuleContext</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></DL>
+
+<P>
+DefaultModuleContext.java
+
+
+ Created: Tue May 23 15:03:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultModuleContext.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html#DefaultModuleContext(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleStorageStructure)">DefaultModuleContext</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A> struct)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html#getConfig()">getConfig</A></B>()</CODE>
+
+<BR>
+ Returns an object representing the configuration of the module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ Returns the modules identifier.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.module.ModuleContext"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getModule()">getModule</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getModuleFactory()">getModuleFactory</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getRequiredModules()">getRequiredModules</A>, <A HREF="../../../../../uk/ac/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultModuleContext(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleStorageStructure)"><!-- --></A><H3>
+DefaultModuleContext</H3>
+<PRE>
+public <B>DefaultModuleContext</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html">ModuleStorageStructure</A> struct)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></CODE></B></DD>
+<DD>Returns the modules identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getIdentifier()">getIdentifier</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfig()"><!-- --></A><H3>
+getConfig</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getConfig</B>()</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></CODE></B></DD>
+<DD>Returns an object representing the configuration of the module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getConfig()">getConfig</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the configuration</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultModuleContext.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html b/doc/javadoc/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html
new file mode 100644
index 0000000..d9d934c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html
@@ -0,0 +1,631 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:22 BST 2002 -->
+<TITLE>
+DefaultModuleFactoryInstance
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultModuleFactoryInstance";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultModuleFactoryInstance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class DefaultModuleFactoryInstance</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.DefaultModuleFactoryInstance</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.html">CinemaModuleFactoryInstance</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultModuleFactoryInstance</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></DL>
+
+<P>
+DefaultModuleFactoryInstance.java
+
+
+ Created: Thu May 11 13:02:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultModuleFactoryInstance.java,v 1.13 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#DefaultModuleFactoryInstance()">DefaultModuleFactoryInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Adds an identifier to the factory storage mechanism.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] identifiers)</CODE>
+
+<BR>
+ Adds identifiers to the factory storage mechanism.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module)">addRequiredModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> reqMod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#addRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module[])">addRequiredModules</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A>[] reqMods)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)">getConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the config object a given module</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the module, given the module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)">getRequiredModules</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the modules required by the given module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)">isModuleAvailable</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns whether a module is available for use.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Loads the module associated with a particular identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#resolveClassName(java.lang.String)">resolveClassName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> classname)</CODE>
+
+<BR>
+ Resolves a classname of a module into the module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#resolveModuleName(java.lang.String)">resolveModuleName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</CODE>
+
+<BR>
+ Resolve a module name into a ModuleIdentifier</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)">setConcreteIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> abstractIdentifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> concreteIdentifier)</CODE>
+
+<BR>
+ Set the concrete identifier for a given abstract identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">setConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ Sets the config to a particular module described by an identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html#setModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module)">setModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultModuleFactoryInstance()"><!-- --></A><H3>
+DefaultModuleFactoryInstance</H3>
+<PRE>
+public <B>DefaultModuleFactoryInstance</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="load(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+load</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>load</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Loads the module associated with a particular identifier. This
+ will include a call to the load method of the module. It should
+ also subsequently check that all requried modules are loaded as
+ well.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+addIdentifier</H3>
+<PRE>
+public void <B>addIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Adds an identifier to the factory storage mechanism.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])"><!-- --></A><H3>
+addIdentifier</H3>
+<PRE>
+public void <B>addIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] identifiers)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Adds identifiers to the factory storage mechanism.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifiers</CODE> - an array of identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveModuleName(java.lang.String)"><!-- --></A><H3>
+resolveModuleName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveModuleName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Resolve a module name into a ModuleIdentifier
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveModuleName(java.lang.String)">resolveModuleName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>moduleName</CODE> - the name of the module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveClassName(java.lang.String)"><!-- --></A><H3>
+resolveClassName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveClassName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> classname)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Resolves a classname of a module into the module identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveClassName(java.lang.String)">resolveClassName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> module)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns the module, given the module identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the module
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module[])"><!-- --></A><H3>
+addRequiredModules</H3>
+<PRE>
+public void <B>addRequiredModules</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A>[] reqMods)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+addRequiredModule</H3>
+<PRE>
+public void <B>addRequiredModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> reqMod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getRequiredModules</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A> <B>getRequiredModules</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns the modules required by the given module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)">getRequiredModules</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier of the module of interest
+<DT><B>Returns:</B><DD>the required modules</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><!-- --></A><H3>
+setConfig</H3>
+<PRE>
+public void <B>setConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Sets the config to a particular module described by an identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">setConfig</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier<DD><CODE>config</CODE> - the config</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getConfig</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns the config object a given module
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)">getConfig</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+setConcreteIdentifier</H3>
+<PRE>
+public void <B>setConcreteIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> abstractIdentifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> concreteIdentifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Set the concrete identifier for a given abstract identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)">setConcreteIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+isModuleAvailable</H3>
+<PRE>
+public boolean <B>isModuleAvailable</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns whether a module is available for use. This allows the
+ use of optional modules.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)">isModuleAvailable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the availability of the target module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#destroy()">destroy</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultModuleFactoryInstance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/GenericModuleIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/module/GenericModuleIdentifier.html
new file mode 100644
index 0000000..b94e052
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/GenericModuleIdentifier.html
@@ -0,0 +1,318 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:22 BST 2002 -->
+<TITLE>
+GenericModuleIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GenericModuleIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GenericModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class GenericModuleIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.GenericModuleIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>GenericModuleIdentifier</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></DL>
+
+<P>
+GenericModuleIdentifier.java
+
+
+ Created: Mon May 15 16:02:45 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GenericModuleIdentifier.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html#GenericModuleIdentifier(java.lang.String, java.lang.String, boolean)">GenericModuleIdentifier</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName,
+ boolean isInterface)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html#getClassName()">getClassName</A></B>()</CODE>
+
+<BR>
+ Returns the string of the class name.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html#getModuleName()">getModuleName</A></B>()</CODE>
+
+<BR>
+ Returns the name of the module being defined.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html#isInterface()">isInterface</A></B>()</CODE>
+
+<BR>
+ Returns whether this module is an interface.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GenericModuleIdentifier(java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>
+GenericModuleIdentifier</H3>
+<PRE>
+public <B>GenericModuleIdentifier</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName,
+ boolean isInterface)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isInterface()"><!-- --></A><H3>
+isInterface</H3>
+<PRE>
+public boolean <B>isInterface</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></B></DD>
+<DD>Returns whether this module is an interface.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#isInterface()">isInterface</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>whether this module is an interface.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getClassName()"><!-- --></A><H3>
+getClassName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getClassName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></B></DD>
+<DD>Returns the string of the class name.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#getClassName()">getClassName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the class name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModuleName()"><!-- --></A><H3>
+getModuleName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getModuleName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></B></DD>
+<DD>Returns the name of the module being defined.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#getModuleName()">getModuleName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GenericModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/Module.html b/doc/javadoc/uk/ac/man/bioinf/module/Module.html
new file mode 100644
index 0000000..801e414
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/Module.html
@@ -0,0 +1,713 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:22 BST 2002 -->
+<TITLE>
+Module
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Module";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Module.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class Module</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.Module</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.html">CinemaCoreGui</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.html">CinemaDebug</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.html">CinemaDebug</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.html">CinemaInvoker</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/shared/CinemaSh [...]
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>Module</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Module.java
+
+ Represents a module, the main constituent of a modular
+ architectured program. It is associated with the module identifier
+ and context classes.
+
+ Created: Wed Apr 19 14:17:05 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Module.java,v 1.10 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#Module()">Module</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.beans.PropertyChangeListener)">addPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">addPropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ The method called, from an external source, to remove this module
+ and prepare it for garbage collection.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#finalize()">finalize</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#firePropertyChange(java.beans.PropertyChangeEvent)">firePropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#firePropertyChange(java.lang.String, int, int)">firePropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ int oldValue,
+ int newValue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)">firePropertyChange</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> oldValue,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> newValue)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#getContext()">getContext</A></B>()</CODE>
+
+<BR>
+ Returns the modules context.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ Returns a module identifier for this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredIdentifiers()">getRequiredIdentifiers</A></B>()</CODE>
+
+<BR>
+ Returns the module identifiers for the required modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getRequiredModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#getRequiredModules()">getRequiredModules</A></B>()</CODE>
+
+<BR>
+ Returns the required modules for this module (ie: the modules
+ that are necessary in order for this module to function).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#getVersion()">getVersion</A></B>()</CODE>
+
+<BR>
+ Returns the version of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#hasListeners(java.lang.String)">hasListeners</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#isDestroyed()">isDestroyed</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#isStarted()">isStarted</A></B>()</CODE>
+
+<BR>
+ Returns whether the module has been started (ie: the start method
+ run).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#load()">load</A></B>()</CODE>
+
+<BR>
+ The method called for the load of this module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#removePropertyChangeListener(java.beans.PropertyChangeListener)">removePropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)">removePropertyChangeListener</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#runStart()">runStart</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#setContext(uk.ac.man.bioinf.module.ModuleContext)">setContext</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/Module.html#start()">start</A></B>()</CODE>
+
+<BR>
+ The method called externally to initiate the modules function.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="Module()"><!-- --></A><H3>
+Module</H3>
+<PRE>
+public <B>Module</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD>Returns a module identifier for this module. Simply performs a
+ delegation to the module context.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>this modules identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModules()"><!-- --></A><H3>
+getRequiredModules</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A> <B>getRequiredModules</B>()</PRE>
+<DL>
+<DD>Returns the required modules for this module (ie: the modules
+ that are necessary in order for this module to function). Simple
+ delegation to the module context.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required modules</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getRequiredModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getRequiredModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredIdentifiers()"><!-- --></A><H3>
+getRequiredIdentifiers</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html">ModuleIdentifierList</A> <B>getRequiredIdentifiers</B>()</PRE>
+<DL>
+<DD>Returns the module identifiers for the required modules. This
+ places a call on getRequiredModules, which is delegated to the
+ module context. It may require over-riding inorder to improve the
+ efficiency of the method.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the required module identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getContext()"><!-- --></A><H3>
+getContext</H3>
+<PRE>
+public final <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> <B>getContext</B>()</PRE>
+<DL>
+<DD>Returns the modules context.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the modules context</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setContext(uk.ac.man.bioinf.module.ModuleContext)"><!-- --></A><H3>
+setContext</H3>
+<PRE>
+public final void <B>setContext</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getVersion()"><!-- --></A><H3>
+getVersion</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getVersion</B>()</PRE>
+<DL>
+<DD>Returns the version of this module.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the version</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load()"><!-- --></A><H3>
+load</H3>
+<PRE>
+public void <B>load</B>()
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD>The method called for the load of this module.
+<P>
+<DD><DL>
+
+<DT><B>Throws:</B>
+<DD><CODE>ModuleLoadException</CODE> - if a loading error occurs
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="start()"><!-- --></A><H3>
+start</H3>
+<PRE>
+public void <B>start</B>()</PRE>
+<DL>
+<DD>The method called externally to initiate the modules function.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="runStart()"><!-- --></A><H3>
+runStart</H3>
+<PRE>
+public void <B>runStart</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isStarted()"><!-- --></A><H3>
+isStarted</H3>
+<PRE>
+public final boolean <B>isStarted</B>()</PRE>
+<DL>
+<DD>Returns whether the module has been started (ie: the start method
+ run).
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>T/F status of call on start() method</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isDestroyed()"><!-- --></A><H3>
+isDestroyed</H3>
+<PRE>
+public boolean <B>isDestroyed</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD>The method called, from an external source, to remove this module
+ and prepare it for garbage collection.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="finalize()"><!-- --></A><H3>
+finalize</H3>
+<PRE>
+public void <B>finalize</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addPropertyChangeListener(java.beans.PropertyChangeListener)"><!-- --></A><H3>
+addPropertyChangeListener</H3>
+<PRE>
+public void <B>addPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removePropertyChangeListener(java.beans.PropertyChangeListener)"><!-- --></A><H3>
+removePropertyChangeListener</H3>
+<PRE>
+public void <B>removePropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addPropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><!-- --></A><H3>
+addPropertyChangeListener</H3>
+<PRE>
+public void <B>addPropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removePropertyChangeListener(java.lang.String, java.beans.PropertyChangeListener)"><!-- --></A><H3>
+removePropertyChangeListener</H3>
+<PRE>
+public void <B>removePropertyChangeListener</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeListener.html">PropertyChangeListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firePropertyChange(java.lang.String, java.lang.Object, java.lang.Object)"><!-- --></A><H3>
+firePropertyChange</H3>
+<PRE>
+protected void <B>firePropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> oldValue,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> newValue)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firePropertyChange(java.lang.String, int, int)"><!-- --></A><H3>
+firePropertyChange</H3>
+<PRE>
+protected void <B>firePropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName,
+ int oldValue,
+ int newValue)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="firePropertyChange(java.beans.PropertyChangeEvent)"><!-- --></A><H3>
+firePropertyChange</H3>
+<PRE>
+protected void <B>firePropertyChange</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/beans/PropertyChangeEvent.html">PropertyChangeEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="hasListeners(java.lang.String)"><!-- --></A><H3>
+hasListeners</H3>
+<PRE>
+public boolean <B>hasListeners</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyName)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Module.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleContext.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleContext.html
new file mode 100644
index 0000000..2383f08
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleContext.html
@@ -0,0 +1,437 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:22 BST 2002 -->
+<TITLE>
+ModuleContext
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleContext";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleContext.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class ModuleContext</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.ModuleContext</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html">DefaultModuleContext</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>ModuleContext</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ModuleContext.java
+
+ Gives context to a module (e.g: configuration information).
+
+ Created: Tue Apr 18 19:17:55 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleContext.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#ModuleContext()">ModuleContext</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getConfig()">getConfig</A></B>()</CODE>
+
+<BR>
+ Returns an object representing the configuration of the module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ Returns the modules identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getModule()">getModule</A></B>()</CODE>
+
+<BR>
+ Returns the associated module for this context.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns a module by interfacing with the ModuleHandlerFactory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getModuleFactory()">getModuleFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#getRequiredModules()">getRequiredModules</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)">isModuleAvailable</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns whether a module is available for use, given the
+ identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#resolveModuleName(java.lang.String)">resolveModuleName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</CODE>
+
+<BR>
+ This method resolves a module name into a ModuleIdentifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html#setModuleFactory(uk.ac.man.bioinf.module.ModuleFactoryInstance)">setModuleFactory</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A> moduleFactory)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ModuleContext()"><!-- --></A><H3>
+ModuleContext</H3>
+<PRE>
+public <B>ModuleContext</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModuleFactory(uk.ac.man.bioinf.module.ModuleFactoryInstance)"><!-- --></A><H3>
+setModuleFactory</H3>
+<PRE>
+public void <B>setModuleFactory</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A> moduleFactory)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModuleFactory()"><!-- --></A><H3>
+getModuleFactory</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A> <B>getModuleFactory</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+isModuleAvailable</H3>
+<PRE>
+public boolean <B>isModuleAvailable</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD>Returns whether a module is available for use, given the
+ identifier. Allows for optional modules.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier for the optional module
+<DT><B>Returns:</B><DD>the availability of the module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD>Returns a module by interfacing with the ModuleHandlerFactory. It
+ is designed to allow use of optional modules.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the module
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveModuleName(java.lang.String)"><!-- --></A><H3>
+resolveModuleName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveModuleName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</PRE>
+<DL>
+<DD>This method resolves a module name into a ModuleIdentifier. Generally
+ speaking this method is not the preferred mechanisms for getting a
+ ModuleIdentifier. If a ModuleIdentifier extends
+ AbstractEnumeratedModuleIdentifier, then they can be directly accessed in a
+ way which is compile time type safe.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>moduleName</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModule()"><!-- --></A><H3>
+getModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getModule</B>()
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD>Returns the associated module for this context.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModules()"><!-- --></A><H3>
+getRequiredModules</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A> <B>getRequiredModules</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public abstract <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD>Returns the modules identifier.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfig()"><!-- --></A><H3>
+getConfig</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getConfig</B>()</PRE>
+<DL>
+<DD>Returns an object representing the configuration of the module.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the configuration</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleContext.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleException.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleException.html
new file mode 100644
index 0000000..1d7a580
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleException.html
@@ -0,0 +1,350 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+ModuleException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/module/NoSuchRequiredModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class ModuleException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.ModuleException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ModuleException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A></DL>
+
+<P>
+ModuleException.java
+
+ An exception thrown if a module does not load sucessfully.
+
+ Created: Tue May 9 18:45:35 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleException.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.module.ModuleException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#ModuleException(uk.ac.man.bioinf.module.ModuleExceptionType)">ModuleException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> id)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.String)">ModuleException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.String, uk.ac.man.bioinf.module.ModuleExceptionType)">ModuleException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> id)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.String, uk.ac.man.bioinf.module.ModuleExceptionType, java.lang.Throwable)">ModuleException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> id,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> throwable)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#ModuleException(java.lang.Throwable)">ModuleException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> throwable)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#getID()">getID</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html#getThrowable()">getThrowable</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ModuleException(java.lang.String)"><!-- --></A><H3>
+ModuleException</H3>
+<PRE>
+public <B>ModuleException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ModuleException(uk.ac.man.bioinf.module.ModuleExceptionType)"><!-- --></A><H3>
+ModuleException</H3>
+<PRE>
+public <B>ModuleException</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> id)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ModuleException(java.lang.Throwable)"><!-- --></A><H3>
+ModuleException</H3>
+<PRE>
+public <B>ModuleException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> throwable)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ModuleException(java.lang.String, uk.ac.man.bioinf.module.ModuleExceptionType)"><!-- --></A><H3>
+ModuleException</H3>
+<PRE>
+public <B>ModuleException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> id)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ModuleException(java.lang.String, uk.ac.man.bioinf.module.ModuleExceptionType, java.lang.Throwable)"><!-- --></A><H3>
+ModuleException</H3>
+<PRE>
+public <B>ModuleException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> id,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> throwable)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getThrowable()"><!-- --></A><H3>
+getThrowable</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> <B>getThrowable</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getID()"><!-- --></A><H3>
+getID</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>getID</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/module/NoSuchRequiredModule.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleExceptionType.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleExceptionType.html
new file mode 100644
index 0000000..d5edbf5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleExceptionType.html
@@ -0,0 +1,342 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+ModuleExceptionType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleExceptionType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleExceptionType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class ModuleExceptionType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.ModuleExceptionType</B>
+</PRE>
+<HR>
+<DL>
+<DT>public final class <B>ModuleExceptionType</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></DL>
+
+<P>
+This class provides an identifier for the module exception that has
+ been thrown, rather than string comparisons needing to be carried
+ out.
+
+
+ Created: Mon May 22 11:26:22 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleExceptionType.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_CLASS_NOT_FOUND">MODULE_CLASS_NOT_FOUND</A></B></CODE>
+
+<BR>
+ The module class was not found in the location stated.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_DOES_NOT_EXIST">MODULE_DOES_NOT_EXIST</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_EXISTS">MODULE_EXISTS</A></B></CODE>
+
+<BR>
+ The module has previously been defined and created.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_INIT_PROBLEM">MODULE_INIT_PROBLEM</A></B></CODE>
+
+<BR>
+ Creating and instantiating the module generated a problem.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html#MODULE_RESOLVE_FAIL">MODULE_RESOLVE_FAIL</A></B></CODE>
+
+<BR>
+ Indicates a failed attempt to resolve a module name</TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MODULE_DOES_NOT_EXIST"><!-- --></A><H3>
+MODULE_DOES_NOT_EXIST</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>MODULE_DOES_NOT_EXIST</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="MODULE_RESOLVE_FAIL"><!-- --></A><H3>
+MODULE_RESOLVE_FAIL</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>MODULE_RESOLVE_FAIL</B></PRE>
+<DL>
+<DD>Indicates a failed attempt to resolve a module name
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="MODULE_EXISTS"><!-- --></A><H3>
+MODULE_EXISTS</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>MODULE_EXISTS</B></PRE>
+<DL>
+<DD>The module has previously been defined and created.
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="MODULE_CLASS_NOT_FOUND"><!-- --></A><H3>
+MODULE_CLASS_NOT_FOUND</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>MODULE_CLASS_NOT_FOUND</B></PRE>
+<DL>
+<DD>The module class was not found in the location stated.
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="MODULE_INIT_PROBLEM"><!-- --></A><H3>
+MODULE_INIT_PROBLEM</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html">ModuleExceptionType</A> <B>MODULE_INIT_PROBLEM</B></PRE>
+<DL>
+<DD>Creating and instantiating the module generated a problem.
+<P>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleExceptionType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleFactoryInstance.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleFactoryInstance.html
new file mode 100644
index 0000000..7f3ff52
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleFactoryInstance.html
@@ -0,0 +1,471 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+ModuleFactoryInstance
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleFactoryInstance";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleFactoryInstance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Interface ModuleFactoryInstance</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html">NullModuleFactory</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ModuleFactoryInstance</B></DL>
+
+<P>
+ModuleFactoryInstance.java
+
+ This interface is designed to provide a means of storing loaded
+ modules and their associated identifiers. It also allows
+ configuration of the module.
+
+ This is instance is called from the ModuleFactory which simply
+ relays the requests here.
+
+ Created: Tue May 9 13:53:20 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleFactoryInstance.java,v 1.10 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Adds an identifier to the factory storage mechanism.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] identifiers)</CODE>
+
+<BR>
+ Adds identifiers to the factory storage mechanism.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)">getConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the config object a given module</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the module, given the module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)">getRequiredModules</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the modules required by the given module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)">isModuleAvailable</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns whether a module is available for use.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Loads the module associated with a particular identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveClassName(java.lang.String)">resolveClassName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className)</CODE>
+
+<BR>
+ Resolves a classname of a module into the module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveModuleName(java.lang.String)">resolveModuleName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</CODE>
+
+<BR>
+ Resolve a module name into a ModuleIdentifier</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)">setConcreteIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> abstractIdentifer,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> concreteIdentifier)</CODE>
+
+<BR>
+ Set the concrete identifier for a given abstract identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">setConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ Sets the config to a particular module described by an identifier.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+isModuleAvailable</H3>
+<PRE>
+public boolean <B>isModuleAvailable</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD>Returns whether a module is available for use. This allows the
+ use of optional modules.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the availability of the target module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD>Returns the module, given the module identifier.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the module
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getRequiredModules</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A> <B>getRequiredModules</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD>Returns the modules required by the given module.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier of the module of interest
+<DT><B>Returns:</B><DD>the required modules</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><!-- --></A><H3>
+setConfig</H3>
+<PRE>
+public void <B>setConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+<DD>Sets the config to a particular module described by an identifier.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier<DD><CODE>config</CODE> - the config</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getConfig</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD>Returns the config object a given module
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+setConcreteIdentifier</H3>
+<PRE>
+public void <B>setConcreteIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> abstractIdentifer,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> concreteIdentifier)</PRE>
+<DL>
+<DD>Set the concrete identifier for a given abstract identifier.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+addIdentifier</H3>
+<PRE>
+public void <B>addIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD>Adds an identifier to the factory storage mechanism.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])"><!-- --></A><H3>
+addIdentifier</H3>
+<PRE>
+public void <B>addIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] identifiers)</PRE>
+<DL>
+<DD>Adds identifiers to the factory storage mechanism.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifiers</CODE> - an array of identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveModuleName(java.lang.String)"><!-- --></A><H3>
+resolveModuleName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveModuleName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</PRE>
+<DL>
+<DD>Resolve a module name into a ModuleIdentifier
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>moduleName</CODE> - the name of the module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveClassName(java.lang.String)"><!-- --></A><H3>
+resolveClassName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveClassName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className)</PRE>
+<DL>
+<DD>Resolves a classname of a module into the module identifier.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+load</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>load</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD>Loads the module associated with a particular identifier. This
+ will include a call to the load method of the module. It should
+ also subsequently check that all requried modules are loaded as
+ well.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD>Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleFactoryInstance.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleIdentifier.html
new file mode 100644
index 0000000..8f7ad9b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleIdentifier.html
@@ -0,0 +1,262 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:21 BST 2002 -->
+<TITLE>
+ModuleIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Interface ModuleIdentifier</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html">GenericModuleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ModuleIdentifier</B></DL>
+
+<P>
+ModuleIdentifier.java
+
+ A thin tag for a module, rather than banding round modules.
+
+ Created: Wed Apr 26 17:05:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleIdentifier.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#getClassName()">getClassName</A></B>()</CODE>
+
+<BR>
+ Returns the string of the class name.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#getModuleName()">getModuleName</A></B>()</CODE>
+
+<BR>
+ Returns the name of the module being defined.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html#isInterface()">isInterface</A></B>()</CODE>
+
+<BR>
+ Returns whether this module is an interface.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isInterface()"><!-- --></A><H3>
+isInterface</H3>
+<PRE>
+public boolean <B>isInterface</B>()</PRE>
+<DL>
+<DD>Returns whether this module is an interface.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>whether this module is an interface.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getClassName()"><!-- --></A><H3>
+getClassName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getClassName</B>()</PRE>
+<DL>
+<DD>Returns the string of the class name.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the class name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModuleName()"><!-- --></A><H3>
+getModuleName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getModuleName</B>()</PRE>
+<DL>
+<DD>Returns the name of the module being defined.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleIdentifierList.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleIdentifierList.html
new file mode 100644
index 0000000..3fbef52
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleIdentifierList.html
@@ -0,0 +1,454 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+ModuleIdentifierList
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleIdentifierList";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleIdentifierList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class ModuleIdentifierList</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.ModuleIdentifierList</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ModuleIdentifierList</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+To provide a list of module identifiers in a type safe manor. This
+ is basically a thin wrapper to list, specially targeted for
+ module identifiers.
+
+
+ Created: Wed May 24 15:06:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleIdentifierList.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#ModuleIdentifierList(java.util.List)">ModuleIdentifierList</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> list)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#add(uk.ac.man.bioinf.module.ModuleIdentifier)">add</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</CODE>
+
+<BR>
+ Adds a module identifier to the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#clear()">clear</A></B>()</CODE>
+
+<BR>
+ Clear the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#contains(uk.ac.man.bioinf.module.ModuleIdentifier)">contains</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</CODE>
+
+<BR>
+ Returns whether a module identifier is contained in this list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#get(int)">get</A></B>(int i)</CODE>
+
+<BR>
+ Returns the module identifier at a given index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#indexOf(uk.ac.man.bioinf.module.ModuleIdentifier)">indexOf</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</CODE>
+
+<BR>
+ Returns the index of a module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#isEmpty()">isEmpty</A></B>()</CODE>
+
+<BR>
+ Returns whether the list is empty.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#remove(int)">remove</A></B>(int i)</CODE>
+
+<BR>
+ Removes a module identifier at a specific index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#remove(uk.ac.man.bioinf.module.ModuleIdentifier)">remove</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</CODE>
+
+<BR>
+ Removes a module identifier from the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#size()">size</A></B>()</CODE>
+
+<BR>
+ Returns the number of module identifiers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html#toArray()">toArray</A></B>()</CODE>
+
+<BR>
+ Returns an array of module identifiers.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ModuleIdentifierList(java.util.List)"><!-- --></A><H3>
+ModuleIdentifierList</H3>
+<PRE>
+public <B>ModuleIdentifierList</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> list)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="add(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public boolean <B>add</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</PRE>
+<DL>
+<DD>Adds a module identifier to the list.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the success of the addition</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clear()"><!-- --></A><H3>
+clear</H3>
+<PRE>
+public void <B>clear</B>()</PRE>
+<DL>
+<DD>Clear the list.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="contains(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+contains</H3>
+<PRE>
+public boolean <B>contains</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</PRE>
+<DL>
+<DD>Returns whether a module identifier is contained in this list.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the query module identifier
+<DT><B>Returns:</B><DD>T/F exists</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="get(int)"><!-- --></A><H3>
+get</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>get</B>(int i)</PRE>
+<DL>
+<DD>Returns the module identifier at a given index.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>i</CODE> - the index
+<DT><B>Returns:</B><DD>the module identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="indexOf(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+indexOf</H3>
+<PRE>
+public int <B>indexOf</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</PRE>
+<DL>
+<DD>Returns the index of a module identifier.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the index</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isEmpty()"><!-- --></A><H3>
+isEmpty</H3>
+<PRE>
+public boolean <B>isEmpty</B>()</PRE>
+<DL>
+<DD>Returns whether the list is empty.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>T/F is the list empty</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(int)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>remove</B>(int i)</PRE>
+<DL>
+<DD>Removes a module identifier at a specific index.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>i</CODE> - the index of the module identifier
+<DT><B>Returns:</B><DD>the module identifier removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public boolean <B>remove</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> m)</PRE>
+<DL>
+<DD>Removes a module identifier from the list.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the module identifier to be removed
+<DT><B>Returns:</B><DD>the success</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD>Returns the number of module identifiers.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the size of the list</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toArray()"><!-- --></A><H3>
+toArray</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] <B>toArray</B>()</PRE>
+<DL>
+<DD>Returns an array of module identifiers.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module identifiers</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleIdentifierList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleList.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleList.html
new file mode 100644
index 0000000..32580a8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleList.html
@@ -0,0 +1,453 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+ModuleList
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleList";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class ModuleList</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.ModuleList</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ModuleList</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+To provide a list of modules in a type safe manor. This is
+ basically a thin wrapper to list, specially targeted for modules.
+
+
+ Created: Wed May 24 15:06:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleList.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#ModuleList(java.util.List)">ModuleList</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> list)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#add(uk.ac.man.bioinf.module.Module)">add</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</CODE>
+
+<BR>
+ Adds a module to the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#clear()">clear</A></B>()</CODE>
+
+<BR>
+ Clear the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#contains(uk.ac.man.bioinf.module.Module)">contains</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</CODE>
+
+<BR>
+ Returns whether a module is contained in this list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#get(int)">get</A></B>(int i)</CODE>
+
+<BR>
+ Returns the module at a given index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#indexOf(uk.ac.man.bioinf.module.Module)">indexOf</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</CODE>
+
+<BR>
+ Returns the index of a module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#isEmpty()">isEmpty</A></B>()</CODE>
+
+<BR>
+ Returns whether the list is empty.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#remove(int)">remove</A></B>(int i)</CODE>
+
+<BR>
+ Removes a module at a specific index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#remove(uk.ac.man.bioinf.module.Module)">remove</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</CODE>
+
+<BR>
+ Removes a module from the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#size()">size</A></B>()</CODE>
+
+<BR>
+ Returns the number of modules.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html#toArray()">toArray</A></B>()</CODE>
+
+<BR>
+ Returns an array of modules.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ModuleList(java.util.List)"><!-- --></A><H3>
+ModuleList</H3>
+<PRE>
+public <B>ModuleList</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/List.html">List</A> list)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="add(uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public boolean <B>add</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</PRE>
+<DL>
+<DD>Adds a module to the list.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the module
+<DT><B>Returns:</B><DD>the success of the addition</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clear()"><!-- --></A><H3>
+clear</H3>
+<PRE>
+public void <B>clear</B>()</PRE>
+<DL>
+<DD>Clear the list.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="contains(uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+contains</H3>
+<PRE>
+public boolean <B>contains</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</PRE>
+<DL>
+<DD>Returns whether a module is contained in this list.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the query module
+<DT><B>Returns:</B><DD>T/F exists</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="get(int)"><!-- --></A><H3>
+get</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>get</B>(int i)</PRE>
+<DL>
+<DD>Returns the module at a given index.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>i</CODE> - the index
+<DT><B>Returns:</B><DD>the module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="indexOf(uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+indexOf</H3>
+<PRE>
+public int <B>indexOf</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</PRE>
+<DL>
+<DD>Returns the index of a module.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the module
+<DT><B>Returns:</B><DD>the index</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isEmpty()"><!-- --></A><H3>
+isEmpty</H3>
+<PRE>
+public boolean <B>isEmpty</B>()</PRE>
+<DL>
+<DD>Returns whether the list is empty.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>T/F is the list empty</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(int)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>remove</B>(int i)</PRE>
+<DL>
+<DD>Removes a module at a specific index.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>i</CODE> - the index of the module
+<DT><B>Returns:</B><DD>the module removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public boolean <B>remove</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> m)</PRE>
+<DL>
+<DD>Removes a module from the list.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>m</CODE> - the module to be removed
+<DT><B>Returns:</B><DD>the success</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD>Returns the number of modules.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the size of the list</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toArray()"><!-- --></A><H3>
+toArray</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A>[] <B>toArray</B>()</PRE>
+<DL>
+<DD>Returns an array of modules.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the modules</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/ModuleStorageStructure.html b/doc/javadoc/uk/ac/man/bioinf/module/ModuleStorageStructure.html
new file mode 100644
index 0000000..fd659a3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/ModuleStorageStructure.html
@@ -0,0 +1,478 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+ModuleStorageStructure
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModuleStorageStructure";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleStorageStructure.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class ModuleStorageStructure</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.ModuleStorageStructure</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ModuleStorageStructure</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ModuleStorageStructure.java
+
+ Stores the module (if it exists), the context, the module
+ configuration object and the required modules for one module
+ identifier. This class is currently exclusively used in the
+ DefaultModuleFactoryInstance.
+
+ Created: Wed May 10 17:02:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModuleStorageStructure.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#ModuleStorageStructure()">ModuleStorageStructure</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#ModuleStorageStructure(uk.ac.man.bioinf.module.ModuleContext)">ModuleStorageStructure</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#ModuleStorageStructure(uk.ac.man.bioinf.module.ModuleContext, java.lang.Object)">ModuleStorageStructure</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#addRequiredModule(uk.ac.man.bioinf.module.Module)">addRequiredModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> reqMod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#addRequiredModules(uk.ac.man.bioinf.module.Module[])">addRequiredModules</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A>[] reqMods)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#getConcreteIdentifier()">getConcreteIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#getConfig()">getConfig</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#getContext()">getContext</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#getModule()">getModule</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#getRequiredModules()">getRequiredModules</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">setConcreteIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#setConfig(java.lang.Object)">setConfig</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#setContext(uk.ac.man.bioinf.module.ModuleContext)">setContext</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html#setModule(uk.ac.man.bioinf.module.Module)">setModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> module)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ModuleStorageStructure()"><!-- --></A><H3>
+ModuleStorageStructure</H3>
+<PRE>
+public <B>ModuleStorageStructure</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ModuleStorageStructure(uk.ac.man.bioinf.module.ModuleContext)"><!-- --></A><H3>
+ModuleStorageStructure</H3>
+<PRE>
+public <B>ModuleStorageStructure</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ModuleStorageStructure(uk.ac.man.bioinf.module.ModuleContext, java.lang.Object)"><!-- --></A><H3>
+ModuleStorageStructure</H3>
+<PRE>
+public <B>ModuleStorageStructure</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setModule(uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+setModule</H3>
+<PRE>
+public void <B>setModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> module)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html">ModuleException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModule()"><!-- --></A><H3>
+getModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getModule</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addRequiredModules(uk.ac.man.bioinf.module.Module[])"><!-- --></A><H3>
+addRequiredModules</H3>
+<PRE>
+public void <B>addRequiredModules</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A>[] reqMods)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addRequiredModule(uk.ac.man.bioinf.module.Module)"><!-- --></A><H3>
+addRequiredModule</H3>
+<PRE>
+public void <B>addRequiredModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> reqMod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModules()"><!-- --></A><H3>
+getRequiredModules</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A> <B>getRequiredModules</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setContext(uk.ac.man.bioinf.module.ModuleContext)"><!-- --></A><H3>
+setContext</H3>
+<PRE>
+public void <B>setContext</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> context)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getContext()"><!-- --></A><H3>
+getContext</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html">ModuleContext</A> <B>getContext</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConfig(java.lang.Object)"><!-- --></A><H3>
+setConfig</H3>
+<PRE>
+public void <B>setConfig</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfig()"><!-- --></A><H3>
+getConfig</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getConfig</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+setConcreteIdentifier</H3>
+<PRE>
+public void <B>setConcreteIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConcreteIdentifier()"><!-- --></A><H3>
+getConcreteIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>getConcreteIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModuleStorageStructure.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/NoSuchRequiredModule.html b/doc/javadoc/uk/ac/man/bioinf/module/NoSuchRequiredModule.html
new file mode 100644
index 0000000..04c4803
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/NoSuchRequiredModule.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+NoSuchRequiredModule
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoSuchRequiredModule";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchRequiredModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class NoSuchRequiredModule</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.NoSuchRequiredModule</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoSuchRequiredModule</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+NoSuchRequiredModule.java
+
+
+ Created: Mon Nov 13 15:24:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoSuchRequiredModule.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.module.NoSuchRequiredModule">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NoSuchRequiredModule.html#NoSuchRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier)">NoSuchRequiredModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NoSuchRequiredModule.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoSuchRequiredModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+NoSuchRequiredModule</H3>
+<PRE>
+public <B>NoSuchRequiredModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> ident)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchRequiredModule.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/NullModuleFactory.html b/doc/javadoc/uk/ac/man/bioinf/module/NullModuleFactory.html
new file mode 100644
index 0000000..b78f1cd
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/NullModuleFactory.html
@@ -0,0 +1,578 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:23 BST 2002 -->
+<TITLE>
+NullModuleFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NullModuleFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullModuleFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.module</FONT>
+<BR>
+Class NullModuleFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.module.NullModuleFactory</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.html">XMLLoadingTest</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NullModuleFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></DL>
+
+<P>
+NullModuleFactory.java
+
+ This class does precisely nothing, but in a very special way.....
+
+ Created: Mon May 15 15:03:40 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NullModuleFactory.java,v 1.10 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#NullModuleFactory()">NullModuleFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">addConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Adds an identifier to the factory storage mechanism.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] identifiers)</CODE>
+
+<BR>
+ Adds identifiers to the factory storage mechanism.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#destroy()">destroy</A></B>()</CODE>
+
+<BR>
+ Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)">getConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> mod)</CODE>
+
+<BR>
+ Returns the config object a given module</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the module, given the module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)">getRequiredModules</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns the modules required by the given module.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)">isModuleAvailable</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Returns whether a module is available for use.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</CODE>
+
+<BR>
+ Loads the module associated with a particular identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#resolveClassName(java.lang.String)">resolveClassName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className)</CODE>
+
+<BR>
+ Resolves a classname of a module into the module identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#resolveModuleName(java.lang.String)">resolveModuleName</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</CODE>
+
+<BR>
+ Resolve a module name into a ModuleIdentifier</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)">setConcreteIdentifier</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> abstractIdentifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> concreteIdentifier)</CODE>
+
+<BR>
+ Set the concrete identifier for a given abstract identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/module/NullModuleFactory.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">setConfig</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> mod,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</CODE>
+
+<BR>
+ Sets the config to a particular module described by an identifier.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NullModuleFactory()"><!-- --></A><H3>
+NullModuleFactory</H3>
+<PRE>
+public <B>NullModuleFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+isModuleAvailable</H3>
+<PRE>
+public boolean <B>isModuleAvailable</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns whether a module is available for use. This allows the
+ use of optional modules.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#isModuleAvailable(uk.ac.man.bioinf.module.ModuleIdentifier)">isModuleAvailable</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the availability of the target module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModule(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getModule</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>getModule</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns the module, given the module identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getModule(uk.ac.man.bioinf.module.ModuleIdentifier)">getModule</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier
+<DT><B>Returns:</B><DD>the module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getRequiredModules</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html">ModuleList</A> <B>getRequiredModules</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns the modules required by the given module.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getRequiredModules(uk.ac.man.bioinf.module.ModuleIdentifier)">getRequiredModules</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the module identifier of the module of interest
+<DT><B>Returns:</B><DD>the required modules</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+addIdentifier</H3>
+<PRE>
+public void <B>addIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Adds an identifier to the factory storage mechanism.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier)">addIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])"><!-- --></A><H3>
+addIdentifier</H3>
+<PRE>
+public void <B>addIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>[] identifiers)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Adds identifiers to the factory storage mechanism.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#addIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier[])">addIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifiers</CODE> - an array of identifiers</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><!-- --></A><H3>
+addConfig</H3>
+<PRE>
+public void <B>addConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="load(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+load</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/Module.html">Module</A> <B>load</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> identifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Loads the module associated with a particular identifier. This
+ will include a call to the load method of the module. It should
+ also subsequently check that all requried modules are loaded as
+ well.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#load(uk.ac.man.bioinf.module.ModuleIdentifier)">load</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>identifier</CODE> - the identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)"><!-- --></A><H3>
+setConfig</H3>
+<PRE>
+public void <B>setConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> mod,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> config)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Sets the config to a particular module described by an identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConfig(uk.ac.man.bioinf.module.ModuleIdentifier, java.lang.Object)">setConfig</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mod</CODE> - the identifier<DD><CODE>config</CODE> - the config</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+getConfig</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>getConfig</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> mod)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Returns the config object a given module
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#getConfig(uk.ac.man.bioinf.module.ModuleIdentifier)">getConfig</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveModuleName(java.lang.String)"><!-- --></A><H3>
+resolveModuleName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveModuleName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> moduleName)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Resolve a module name into a ModuleIdentifier
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveModuleName(java.lang.String)">resolveModuleName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>moduleName</CODE> - the name of the module</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resolveClassName(java.lang.String)"><!-- --></A><H3>
+resolveClassName</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> <B>resolveClassName</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> className)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Resolves a classname of a module into the module identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#resolveClassName(java.lang.String)">resolveClassName</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the module identifier</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="destroy()"><!-- --></A><H3>
+destroy</H3>
+<PRE>
+public void <B>destroy</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Destroy all of the module instances, and remove all the internal
+ data structures of this Factory.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#destroy()">destroy</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)"><!-- --></A><H3>
+setConcreteIdentifier</H3>
+<PRE>
+public void <B>setConcreteIdentifier</B>(<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> abstractIdentifier,
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A> concreteIdentifier)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></B></DD>
+<DD>Set the concrete identifier for a given abstract identifier.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html#setConcreteIdentifier(uk.ac.man.bioinf.module.ModuleIdentifier, uk.ac.man.bioinf.module.ModuleIdentifier)">setConcreteIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NullModuleFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/module/package-frame.html
new file mode 100644
index 0000000..30da791
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/package-frame.html
@@ -0,0 +1,78 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.module()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.module()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../uk/ac/man/bioinf/module/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.module</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ModuleFactoryInstance.html" TARGET="classFrame"><I>ModuleFactoryInstance</I></A>
+<BR>
+<A HREF="ModuleIdentifier.html" TARGET="classFrame"><I>ModuleIdentifier</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractEnumeratedModuleIdentifier.html" TARGET="classFrame">AbstractEnumeratedModuleIdentifier</A>
+<BR>
+<A HREF="DefaultModuleContext.html" TARGET="classFrame">DefaultModuleContext</A>
+<BR>
+<A HREF="DefaultModuleFactoryInstance.html" TARGET="classFrame">DefaultModuleFactoryInstance</A>
+<BR>
+<A HREF="GenericModuleIdentifier.html" TARGET="classFrame">GenericModuleIdentifier</A>
+<BR>
+<A HREF="Module.html" TARGET="classFrame">Module</A>
+<BR>
+<A HREF="ModuleContext.html" TARGET="classFrame">ModuleContext</A>
+<BR>
+<A HREF="ModuleExceptionType.html" TARGET="classFrame">ModuleExceptionType</A>
+<BR>
+<A HREF="ModuleIdentifierList.html" TARGET="classFrame">ModuleIdentifierList</A>
+<BR>
+<A HREF="ModuleList.html" TARGET="classFrame">ModuleList</A>
+<BR>
+<A HREF="ModuleStorageStructure.html" TARGET="classFrame">ModuleStorageStructure</A>
+<BR>
+<A HREF="NullModuleFactory.html" TARGET="classFrame">NullModuleFactory</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ModuleException.html" TARGET="classFrame">ModuleException</A>
+<BR>
+<A HREF="NoSuchRequiredModule.html" TARGET="classFrame">NoSuchRequiredModule</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/module/package-summary.html
new file mode 100644
index 0000000..c526267
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/package-summary.html
@@ -0,0 +1,245 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.module()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.module()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.module
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleFactoryInstance.html"><I>ModuleFactoryInstance</I></A></B></TD>
+<TD>ModuleFactoryInstance.java
+
+ This interface is designed to provide a means of storing loaded
+ modules and their associated identifiers.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleIdentifier.html"><I>ModuleIdentifier</I></A></B></TD>
+<TD>ModuleIdentifier.java
+
+ A thin tag for a module, rather than banding round modules.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A></B></TD>
+<TD>AbstractEnumeratedModuleIdentifier.java
+
+
+ Created: Sun May 7 17:42:13 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultModuleContext.html">DefaultModuleContext</A></B></TD>
+<TD>DefaultModuleContext.java
+
+
+ Created: Tue May 23 15:03:25 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultModuleFactoryInstance.html">DefaultModuleFactoryInstance</A></B></TD>
+<TD>DefaultModuleFactoryInstance.java
+
+
+ Created: Thu May 11 13:02:22 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GenericModuleIdentifier.html">GenericModuleIdentifier</A></B></TD>
+<TD>GenericModuleIdentifier.java
+
+
+ Created: Mon May 15 16:02:45 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Module.html">Module</A></B></TD>
+<TD>Module.java
+
+ Represents a module, the main constituent of a modular
+ architectured program.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleContext.html">ModuleContext</A></B></TD>
+<TD>ModuleContext.java
+
+ Gives context to a module (e.g: configuration information).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleExceptionType.html">ModuleExceptionType</A></B></TD>
+<TD>This class provides an identifier for the module exception that has
+ been thrown, rather than string comparisons needing to be carried
+ out.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleIdentifierList.html">ModuleIdentifierList</A></B></TD>
+<TD>To provide a list of module identifiers in a type safe manor.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleList.html">ModuleList</A></B></TD>
+<TD>To provide a list of modules in a type safe manor.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleStorageStructure.html">ModuleStorageStructure</A></B></TD>
+<TD>ModuleStorageStructure.java
+
+ Stores the module (if it exists), the context, the module
+ configuration object and the required modules for one module
+ identifier.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NullModuleFactory.html">NullModuleFactory</A></B></TD>
+<TD>NullModuleFactory.java
+
+ This class does precisely nothing, but in a very special way.....</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModuleException.html">ModuleException</A></B></TD>
+<TD>ModuleException.java
+
+ An exception thrown if a module does not load sucessfully.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoSuchRequiredModule.html">NoSuchRequiredModule</A></B></TD>
+<TD>NoSuchRequiredModule.java
+
+
+ Created: Mon Nov 13 15:24:02 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/module/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/module/package-tree.html
new file mode 100644
index 0000000..38d025b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/module/package-tree.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.module Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.module Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.module
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html"><B>AbstractEnumeratedModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleExceptionType.html"><B>ModuleExceptionType</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.html"><B>DefaultModuleFactoryInstance</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html">ModuleFactoryInstance</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/GenericModuleIdentifier.html"><B>GenericModuleIdentifier</B></A> (implements uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html">ModuleIdentifier</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/Module.html"><B>Module</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleContext.html"><B>ModuleContext</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/DefaultModuleContext.html"><B>DefaultModuleContext</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifierList.html"><B>ModuleIdentifierList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleList.html"><B>ModuleList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleStorageStructure.html"><B>ModuleStorageStructure</B></A><LI TYPE="circle">class uk.ac.man.bioinf.modul [...]
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleException.html"><B>ModuleException</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/NoSuchRequiredModule.html"><B>NoSuchRequiredModule</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleFactoryInstance.html"><B>ModuleFactoryInstance</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.module.<A HREF="../../../../../uk/ac/man/bioinf/module/ModuleIdentifier.html"><B>ModuleIdentifier</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/io/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/package-frame.html
new file mode 100644
index 0000000..17ffbc2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/package-frame.html
@@ -0,0 +1,32 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../uk/ac/man/bioinf/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Y.html" TARGET="classFrame">Y</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/package-summary.html
new file mode 100644
index 0000000..2a45a17
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/package-summary.html
@@ -0,0 +1,137 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV PACKAGE
+ <A HREF="../../../../uk/ac/man/bioinf/analysis/consensus/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Y.html">Y</A></B></TD>
+<TD>Y.java
+
+ Class created entirely for the purpose of being tab
+ completable.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV PACKAGE
+ <A HREF="../../../../uk/ac/man/bioinf/analysis/consensus/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/package-tree.html
new file mode 100644
index 0000000..603ab79
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/package-tree.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:08 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ <A HREF="../../../../uk/ac/man/bioinf/analysis/consensus/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.<A HREF="../../../../uk/ac/man/bioinf/Y.html"><B>Y</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV
+ <A HREF="../../../../uk/ac/man/bioinf/analysis/consensus/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractEditableSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractEditableSequence.html
new file mode 100644
index 0000000..5c95096
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractEditableSequence.html
@@ -0,0 +1,550 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+AbstractEditableSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractEditableSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEditableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class AbstractEditableSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.AbstractEditableSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"> [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractEditableSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></DL>
+
+<P>
+AbstractEditableSequence.java
+
+ This class provides trivial implementations of all of those methods
+ which can be defined in terms of the others of the EditableSequence
+ interface, and also ensures that the event handling occurs correctly
+
+ Created: Fri Mar 3 12:11:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractEditableSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#AbstractEditableSequence(uk.ac.man.bioinf.sequence.SequenceType)">AbstractEditableSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAt(int)">deleteElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Delete the element at index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAt(int, int)">deleteElementAt</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Delete the elements starting at index for the specified length</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAtQuietly(int)">deleteElementAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ Do the actual deletion but dont do any event signalling.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)">insertElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem,
+ int index)</CODE>
+
+<BR>
+ Provides a trivial implementation of this method by calling
+ multiple single insert methods.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element, int)">insertElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</CODE>
+
+<BR>
+ Insert the element at the specified index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)">insertElementAtQuietly</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element[], int)">setElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem,
+ int index)</CODE>
+
+<BR>
+ Provides a simple implementation of this method by iterating
+ through the element array, and calling the super class
+ method.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element, int)">setElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</CODE>
+
+<BR>
+ Sets the value of the element at the specified index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)">setElementAtQuietly</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk.ac.man.b [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getEl [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#ge [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceLis [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractEditableSequence(uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+AbstractEditableSequence</H3>
+<PRE>
+public <B>AbstractEditableSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+setElementAtQuietly</H3>
+<PRE>
+protected abstract <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>setElementAtQuietly</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAt(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+setElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>setElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></B></DD>
+<DD>Sets the value of the element at the specified index.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element, int)">setElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elem</CODE> - <DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD>the old value
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE> - if some listener doesnt like this</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><!-- --></A><H3>
+setElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>setElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Provides a simple implementation of this method by iterating
+ through the element array, and calling the super class
+ method. Subclasses may override this to provide a more efficient implementation
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element[], int)">setElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elem</CODE> - the elements to set<DD><CODE>index</CODE> - the index at which to start
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+insertElementAtQuietly</H3>
+<PRE>
+protected abstract void <B>insertElementAtQuietly</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAt(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+insertElementAt</H3>
+<PRE>
+public void <B>insertElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></B></DD>
+<DD>Insert the element at the specified index. After insertion
+ getElementAt( index ) will return element, and the sequence will
+ be longer by one
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element, int)">insertElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elem</CODE> - the element to insert<DD><CODE>index</CODE> - the index at which to insert
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><!-- --></A><H3>
+insertElementAt</H3>
+<PRE>
+public void <B>insertElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Provides a trivial implementation of this method by calling
+ multiple single insert methods. Subclasses will almost definately
+ find it more efficient to over ride this method!
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)">insertElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elem</CODE> - <DD><CODE>index</CODE> -
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteElementAtQuietly(int)"><!-- --></A><H3>
+deleteElementAtQuietly</H3>
+<PRE>
+protected abstract <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>deleteElementAtQuietly</B>(int index)</PRE>
+<DL>
+<DD>Do the actual deletion but dont do any event signalling. This
+ enables all the deletions to use this method without causing
+ multiple events for deletions longer than one in length
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the element to delete
+<DT><B>Returns:</B><DD>the element just deleted</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteElementAt(int)"><!-- --></A><H3>
+deleteElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>deleteElementAt</B>(int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></B></DD>
+<DD>Delete the element at index.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int)">deleteElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to delete
+<DT><B>Returns:</B><DD>the element which has just been deleted
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteElementAt(int, int)"><!-- --></A><H3>
+deleteElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>deleteElementAt</B>(int index,
+ int length)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></B></DD>
+<DD>Delete the elements starting at index for the specified length
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int, int)">deleteElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to start at<DD><CODE>length</CODE> - the length to delete
+<DT><B>Returns:</B><DD>the elements just deleted
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEditableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractMutableSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractMutableSequence.html
new file mode 100644
index 0000000..7e313e4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractMutableSequence.html
@@ -0,0 +1,436 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+AbstractMutableSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractMutableSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractMutableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class AbstractMutableSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.AbstractMutableSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractMutableSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A></DL>
+
+<P>
+AbstractMutableSequence.java
+
+
+ Created: Thu Mar 2 20:20:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractMutableSequence.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#AbstractMutableSequence(uk.ac.man.bioinf.sequence.SequenceType)">AbstractMutableSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk.ac.man.bioinf.sequence.event.SequenceEvent)">fireSequenceEvent</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireVetoableSequenceEvent(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">fireVetoableSequenceEvent</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#hasListeners()">hasListeners</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified vetoable sequence listener.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getEl [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#ge [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractMutableSequence(uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+AbstractMutableSequence</H3>
+<PRE>
+public <B>AbstractMutableSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="fireVetoableSequenceEvent(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+fireVetoableSequenceEvent</H3>
+<PRE>
+protected void <B>fireVetoableSequenceEvent</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireSequenceEvent(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+fireSequenceEvent</H3>
+<PRE>
+protected void <B>fireSequenceEvent</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="hasListeners()"><!-- --></A><H3>
+hasListeners</H3>
+<PRE>
+protected boolean <B>hasListeners</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractMutableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractSequence.html
new file mode 100644
index 0000000..69a0493
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/AbstractSequence.html
@@ -0,0 +1,484 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+AbstractSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class AbstractSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.AbstractSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html">DefaultSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequence</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DL>
+
+<P>
+AbstractSequence.java
+
+ Provides some of the methods for sequence. It assumes that the
+ sequence is stored internally as a list of Residues and does all
+ the mapping into chars.
+
+ Created: Thu Mar 2 16:10:51 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequence.java,v 1.7 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#AbstractSequence(uk.ac.man.bioinf.sequence.SequenceType)">AbstractSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</CODE>
+
+<BR>
+ Check if all these elements are of a valid type</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></B>(int index)</CODE>
+
+<BR>
+ Returns the character of an target element.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceAsChars()">getSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of characters.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceIndexException(int)">getSequenceIndexException</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the type of sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceTypeException(uk.ac.man.bioinf.sequence.Element)">getSequenceTypeException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSubSequence(int, int)">getSubSequence</A></B>(int position,
+ int length)</CODE>
+
+<BR>
+ Returns a sub-sequence from the current sequence.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequence(uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+AbstractSequence</H3>
+<PRE>
+public <B>AbstractSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the type of sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubSequence(int, int)"><!-- --></A><H3>
+getSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getSubSequence</B>(int position,
+ int length)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns a sub-sequence from the current sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>position</CODE> - the initial index of the sub-sequence
+<DT><B>Returns:</B><DD>the sub-sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsChars()"><!-- --></A><H3>
+getSequenceAsChars</H3>
+<PRE>
+public char[] <B>getSequenceAsChars</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of characters.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAtAsChar(int)"><!-- --></A><H3>
+getElementAtAsChar</H3>
+<PRE>
+public char <B>getElementAtAsChar</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the character of an target element.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element character</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkSequenceType(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+checkSequenceType</H3>
+<PRE>
+protected void <B>checkSequenceType</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD>Check if all these elements are of a valid type
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE> - if an element is not of a
+ valid type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceTypeException(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+getSequenceTypeException</H3>
+<PRE>
+protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A> <B>getSequenceTypeException</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkSequenceType(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+checkSequenceType</H3>
+<PRE>
+protected void <B>checkSequenceType</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceIndexException(int)"><!-- --></A><H3>
+getSequenceIndexException</H3>
+<PRE>
+protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A> <B>getSequenceIndexException</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkRange(int)"><!-- --></A><H3>
+checkRange</H3>
+<PRE>
+protected void <B>checkRange</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html
new file mode 100644
index 0000000..3fecf9d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+ComplexEditableGappedSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexEditableGappedSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexEditableGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface ComplexEditableGappedSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequ [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ComplexEditableGappedSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/align [...]
+
+<P>
+ComplexEditableGappedSequence.java
+
+
+ Created: Wed Dec 6 20:08:32 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexEditableGappedSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#ge [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceLis [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.ComplexSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAtAsChar(int)">getComplexElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bi [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.EditableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int)">deleteElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int, int)">deleteElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)">insertElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.m [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.GappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGapp [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexEditableGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/DefaultEditableSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/DefaultEditableSequence.html
new file mode 100644
index 0000000..b68c664
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/DefaultEditableSequence.html
@@ -0,0 +1,506 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+DefaultEditableSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultEditableSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultEditableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class DefaultEditableSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">uk.ac.man.bioinf.sequence.AbstractEditableSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.DefaultEditableSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"> [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultEditableSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></DL>
+
+<P>
+DefaultEditableSequence.java
+
+
+ Created: Thu Mar 2 20:27:46 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultEditableSequence.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#DefaultEditableSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultEditableSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> identifier)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#DefaultEditableSequence(uk.ac.man.bioinf.sequence.Sequence)">DefaultEditableSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#DefaultEditableSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.sequence.SequenceType)">DefaultEditableSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#deleteElementAtQuietly(int)">deleteElementAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ Do the actual deletion but dont do any event signalling.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)">insertElementAtQuietly</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)">setElementAtQuietly</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractEditableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAt(int)">deleteElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAt(int, int)">deleteElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)">insertElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSeque [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk.ac.man.b [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getEl [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.EditableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int)">deleteElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int, int)">deleteElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)">insertElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.m [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceLis [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultEditableSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultEditableSequence</H3>
+<PRE>
+public <B>DefaultEditableSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> identifier)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultEditableSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultEditableSequence</H3>
+<PRE>
+public <B>DefaultEditableSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultEditableSequence(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+DefaultEditableSequence</H3>
+<PRE>
+public <B>DefaultEditableSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+setElementAtQuietly</H3>
+<PRE>
+protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>setElementAtQuietly</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)">setElementAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+insertElementAtQuietly</H3>
+<PRE>
+protected void <B>insertElementAtQuietly</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#insertElementAtQuietly(uk.ac.man.bioinf.sequence.Element, int)">insertElementAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteElementAtQuietly(int)"><!-- --></A><H3>
+deleteElementAtQuietly</H3>
+<PRE>
+protected <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>deleteElementAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A></CODE></B></DD>
+<DD>Do the actual deletion but dont do any event signalling. This
+ enables all the deletions to use this method without causing
+ multiple events for deletions longer than one in length
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html#deleteElementAtQuietly(int)">deleteElementAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the element to delete
+<DT><B>Returns:</B><DD>the element just deleted</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultEditableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/DefaultSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/DefaultSequence.html
new file mode 100644
index 0000000..56ab3f8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/DefaultSequence.html
@@ -0,0 +1,385 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+DefaultSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class DefaultSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.DefaultSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></DL>
+
+<P>
+DefaultSequence.java
+
+
+ Created: Thu Mar 2 15:32:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultSequence.java,v 1.8 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)">DefaultSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Sequence)">DefaultSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#DefaultSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.sequence.SequenceType)">DefaultSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getEl [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultSequence</H3>
+<PRE>
+public <B>DefaultSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultSequence</H3>
+<PRE>
+public <B>DefaultSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultSequence</H3>
+<PRE>
+public <B>DefaultSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequence(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+DefaultSequence</H3>
+<PRE>
+public <B>DefaultSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/EditableSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/EditableSequence.html
new file mode 100644
index 0000000..a547b07
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/EditableSequence.html
@@ -0,0 +1,420 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+EditableSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="EditableSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EditableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface EditableSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html">DefaultEditableSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>EditableSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A></DL>
+
+<P>
+EditableSequence.java
+
+
+ Created: Wed Mar 1 19:39:40 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: EditableSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int)">deleteElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Delete the element at index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#deleteElementAt(int, int)">deleteElementAt</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Delete the elements starting at index for the specified length</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)">insertElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element,
+ int index)</CODE>
+
+<BR>
+ Inserts the elements at this position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#insertElementAt(uk.ac.man.bioinf.sequence.Element, int)">insertElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ int index)</CODE>
+
+<BR>
+ Insert the element at the specified index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element[], int)">setElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html#setElementAt(uk.ac.man.bioinf.sequence.Element, int)">setElementAt</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ int index)</CODE>
+
+<BR>
+ Sets the value of the element at the specified index.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#ge [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceLis [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setElementAt(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+setElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>setElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Sets the value of the element at the specified index.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - <DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD>the old value
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the element does not
+ exist (index greater that length + 1 or less than 1)
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE> - if some listener doesnt like this</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><!-- --></A><H3>
+setElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>setElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAt(uk.ac.man.bioinf.sequence.Element, int)"><!-- --></A><H3>
+insertElementAt</H3>
+<PRE>
+public void <B>insertElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Insert the element at the specified index. After insertion
+ getElementAt( index ) will return element, and the sequence will
+ be longer by one
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element to insert<DD><CODE>index</CODE> - the index at which to insert
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertElementAt(uk.ac.man.bioinf.sequence.Element[], int)"><!-- --></A><H3>
+insertElementAt</H3>
+<PRE>
+public void <B>insertElementAt</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element,
+ int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Inserts the elements at this position. If the index is one longer
+ than the length of the sequence the sequence will be extended.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the elements to insert<DD><CODE>index</CODE> - the index at which to insert
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the element does not
+ exist, which will be the case if index is less than 1 or greater
+ than sequence length + 1
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteElementAt(int)"><!-- --></A><H3>
+deleteElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>deleteElementAt</B>(int index)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Delete the element at index.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to delete
+<DT><B>Returns:</B><DD>the element which has just been deleted
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if index is less than 1
+ or greater than the length of the sequence
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteElementAt(int, int)"><!-- --></A><H3>
+deleteElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>deleteElementAt</B>(int index,
+ int length)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Delete the elements starting at index for the specified length
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to start at<DD><CODE>length</CODE> - the length to delete
+<DT><B>Returns:</B><DD>the elements just deleted
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the elements do not all
+ exist, so if index is less than 1, or index + length is greater
+ than the length of the sequence
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EditableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/Element.html b/doc/javadoc/uk/ac/man/bioinf/sequence/Element.html
new file mode 100644
index 0000000..a2c4840
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/Element.html
@@ -0,0 +1,225 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+Element
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Element";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Element.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface Element</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html"> [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.h [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Element</B></DL>
+
+<P>
+Element.java
+
+ This interface defines an element within a sequence. Implementations
+ of this will be immutable after definition. The interface is designed
+ to be as thin as possible. Two equal elements should represent the
+ same biological element.
+
+ Created: Sat Feb 26 18:29:35 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Element.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></B>()</CODE>
+
+<BR>
+ Returns a character representation of this element.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toChar()"><!-- --></A><H3>
+toChar</H3>
+<PRE>
+public char <B>toChar</B>()</PRE>
+<DL>
+<DD>Returns a character representation of this element. This may be
+ non-alphanumeric, and should be unique within a SequenceType.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the char representation<DT><B>See Also:</B><DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><CODE>SequenceType</CODE></A></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Element.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/EmptySequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/EmptySequence.html
new file mode 100644
index 0000000..0e23051
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/EmptySequence.html
@@ -0,0 +1,437 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+EmptySequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="EmptySequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptySequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class EmptySequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.EmptySequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>EmptySequence</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DL>
+
+<P>
+EmptySequence.java
+
+
+ Created: Mon Feb 5 17:53:37 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: EmptySequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getElementAt(int)">getElementAt</A></B>(int param1)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></B>(int param1)</CODE>
+
+<BR>
+ Returns the character of an target element.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getSequenceAsChars()">getSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of characters.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the type of sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html#getSubSequence(int, int)">getSubSequence</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Returns a sub-sequence from the current sequence.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubSequence(int, int)"><!-- --></A><H3>
+getSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getSubSequence</B>(int param1,
+ int param2)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns a sub-sequence from the current sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the initial index of the sub-sequence
+<DT><B>Returns:</B><DD>the sub-sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the type of sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsChars()"><!-- --></A><H3>
+getSequenceAsChars</H3>
+<PRE>
+public char[] <B>getSequenceAsChars</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of characters.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAtAsChar(int)"><!-- --></A><H3>
+getElementAtAsChar</H3>
+<PRE>
+public char <B>getElementAtAsChar</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the character of an target element.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element character</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptySequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html
new file mode 100644
index 0000000..5cbf94e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+InvalidSequenceTypeException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="InvalidSequenceTypeException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvalidSequenceTypeException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class InvalidSequenceTypeException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.InvalidSequenceTypeException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>InvalidSequenceTypeException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+InvalidSequenceTypeException.java
+
+ Exception to signal that an attempt has been made to use a sequence
+ of an invalid type.
+
+ Created: Sat Feb 19 17:36:52 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: InvalidSequenceTypeException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.InvalidSequenceTypeException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html#InvalidSequenceTypeException(java.lang.String)">InvalidSequenceTypeException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="InvalidSequenceTypeException(java.lang.String)"><!-- --></A><H3>
+InvalidSequenceTypeException</H3>
+<PRE>
+public <B>InvalidSequenceTypeException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="InvalidSequenceTypeException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/MutableSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/MutableSequence.html
new file mode 100644
index 0000000..17a985c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/MutableSequence.html
@@ -0,0 +1,219 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+MutableSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="MutableSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MutableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface MutableSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A>, <A HREF="../../. [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusS [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>MutableSequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></DL>
+
+<P>
+MutableSequence.java
+
+ A marker class to present a sequence which can be changed without
+ the necessity for generating a new sequence. By extending
+ SequenceEventProvider, the ability to listen to the sequence has
+ been added.
+
+ Created: Fri Feb 25 20:07:16 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: MutableSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#ge [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceLis [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MutableSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html
new file mode 100644
index 0000000..26916ff
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+NoSuchSequenceElementException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoSuchSequenceElementException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchSequenceElementException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class NoSuchSequenceElementException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.NoSuchSequenceElementException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoSuchSequenceElementException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+NoSuchSequenceElementException.java
+
+
+ Created: Fri Mar 3 12:22:15 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoSuchSequenceElementException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.NoSuchSequenceElementException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException()">NoSuchSequenceElementException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException(uk.ac.man.bioinf.sequence.Sequence, int)">NoSuchSequenceElementException</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException(java.lang.String)">NoSuchSequenceElementException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html#NoSuchSequenceElementException(java.lang.String, uk.ac.man.bioinf.sequence.Sequence, int)">NoSuchSequenceElementException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoSuchSequenceElementException()"><!-- --></A><H3>
+NoSuchSequenceElementException</H3>
+<PRE>
+public <B>NoSuchSequenceElementException</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoSuchSequenceElementException(java.lang.String)"><!-- --></A><H3>
+NoSuchSequenceElementException</H3>
+<PRE>
+public <B>NoSuchSequenceElementException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoSuchSequenceElementException(uk.ac.man.bioinf.sequence.Sequence, int)"><!-- --></A><H3>
+NoSuchSequenceElementException</H3>
+<PRE>
+public <B>NoSuchSequenceElementException</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ int index)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoSuchSequenceElementException(java.lang.String, uk.ac.man.bioinf.sequence.Sequence, int)"><!-- --></A><H3>
+NoSuchSequenceElementException</H3>
+<PRE>
+public <B>NoSuchSequenceElementException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ int index)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchSequenceElementException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/Residue.html b/doc/javadoc/uk/ac/man/bioinf/sequence/Residue.html
new file mode 100644
index 0000000..a29b125
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/Residue.html
@@ -0,0 +1,198 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+Residue
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Residue";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Residue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface Residue</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Residue</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DL>
+
+<P>
+Residue.java
+
+ An interface to represent entirely biological elements.
+
+ Created: Mon Feb 28 12:23:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Residue.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Residue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/Sequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/Sequence.html
new file mode 100644
index 0000000..f6b6370
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/Sequence.html
@@ -0,0 +1,391 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+Sequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Sequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Sequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface Sequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../uk/a [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSeque [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Sequence</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></DL>
+
+<P>
+Sequence.java
+
+ This interface is designed to model a biological sequence. It is
+ non-specific in the manor in which a sequence may be implemented.
+ The default implementation of this sequence will be imutable, and
+ all sequence numbering will start at 1 <b>NOT</b> 0. This may be
+ a set of rules worth following. For a mutable sequence, see the
+ interface MutableSequence.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Sequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><CODE>Created: Fri Feb 25 19:21:55 2000</CODE></A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></B>(int index)</CODE>
+
+<BR>
+ Returns the character of an target element.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of characters.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the type of sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></B>(int from,
+ int length)</CODE>
+
+<BR>
+ Returns a sub-sequence from the current sequence.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSubSequence(int, int)"><!-- --></A><H3>
+getSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getSubSequence</B>(int from,
+ int length)</PRE>
+<DL>
+<DD>Returns a sub-sequence from the current sequence.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>from</CODE> - the initial index of the sub-sequence
+<DT><B>Returns:</B><DD>the sub-sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsChars()"><!-- --></A><H3>
+getSequenceAsChars</H3>
+<PRE>
+public char[] <B>getSequenceAsChars</B>()</PRE>
+<DL>
+<DD>Returns the sequence as an array of characters.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAtAsChar(int)"><!-- --></A><H3>
+getElementAtAsChar</H3>
+<PRE>
+public char <B>getElementAtAsChar</B>(int index)</PRE>
+<DL>
+<DD>Returns the character of an target element.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element character</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD>Returns the type of sequence.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Sequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceException.html
new file mode 100644
index 0000000..373c47b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+SequenceException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class SequenceException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.SequenceException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+SequenceException.java
+
+
+ Created: Thu Mar 2 17:07:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.SequenceException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceException.html#SequenceException(java.lang.String)">SequenceException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceException(java.lang.String)"><!-- --></A><H3>
+SequenceException</H3>
+<PRE>
+public <B>SequenceException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceFactory.html b/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceFactory.html
new file mode 100644
index 0000000..be49c1d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceFactory.html
@@ -0,0 +1,364 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+SequenceFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class SequenceFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.SequenceFactory</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceFactory provides a simple way into the Sequence API. It
+ offers factory methods to create sequences from Strings and
+ Characters. This, combined with the methods in the utility class
+ <code>Sequences</code> is probably all that most users will need.
+
+
+ Created: Tue Nov 14 18:06:37 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+, Crispin Miller</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected static <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html#aa">aa</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html#SequenceFactory()">SequenceFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html#getDNASequence(char[])">getDNASequence</A></B>(char[] dnaSequence)</CODE>
+
+<BR>
+ Create a Sequence representing a DNA sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html#getDNASequence(java.lang.String)">getDNASequence</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> dnaSequence)</CODE>
+
+<BR>
+ Create a Sequence representing a DNA sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html#getProteinSequence(char[])">getProteinSequence</A></B>(char[] proteinSequence)</CODE>
+
+<BR>
+ Create a Sequence representing a protein sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html#getProteinSequence(java.lang.String)">getProteinSequence</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> proteinSequence)</CODE>
+
+<BR>
+ Create a Sequence representing a protein sequence.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="aa"><!-- --></A><H3>
+aa</H3>
+<PRE>
+protected static <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>[] <B>aa</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceFactory()"><!-- --></A><H3>
+SequenceFactory</H3>
+<PRE>
+public <B>SequenceFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getProteinSequence(char[])"><!-- --></A><H3>
+getProteinSequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getProteinSequence</B>(char[] proteinSequence)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD>Create a Sequence representing a protein sequence.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>proteinSequence</CODE> - a character array representing the residues in the sequence - see AminoAcid for more details
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE> - if the input sequence contains an invalid character.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getProteinSequence(java.lang.String)"><!-- --></A><H3>
+getProteinSequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getProteinSequence</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> proteinSequence)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD>Create a Sequence representing a protein sequence.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>proteinSequence</CODE> - represents the residues in the sequence - see AminoAcid for more details
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE> - if the input sequence contains an invalid character.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDNASequence(char[])"><!-- --></A><H3>
+getDNASequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getDNASequence</B>(char[] dnaSequence)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD>Create a Sequence representing a DNA sequence.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>dnaSequence</CODE> - represents the residues in the sequence - see Nucleotide for more details
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE> - if the input sequence contains an invalid character.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDNASequence(java.lang.String)"><!-- --></A><H3>
+getDNASequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getDNASequence</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> dnaSequence)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD>Create a Sequence representing a DNA sequence.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>dnaSequence</CODE> - represents the residues in the sequence - see Nucleotide for more details
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE> - if the input sequence contains an invalid character.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceType.html
new file mode 100644
index 0000000..703c092
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/SequenceType.html
@@ -0,0 +1,413 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:24 BST 2002 -->
+<TITLE>
+SequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Interface SequenceType</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySeq [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceType</B></DL>
+
+<P>
+SequenceType.java
+
+ An interface to represent the type of a sequence (e.g: Protein, DNA).
+
+ Created: Fri Feb 25 20:12:45 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceType.java,v 1.7 2001/05/08 17:47:31 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)">getElementForInt</A></B>(int index)</CODE>
+
+<BR>
+ The inverse of the method getIntForElement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElements()">getElements</A></B>()</CODE>
+
+<BR>
+ Returns all the elements available in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ This method is present as a performance enhancement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the human readable form of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char)">isElement</A></B>(char element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char[])">isElement</A></B>(char[] elements)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#size()">size</A></B>()</CODE>
+
+<BR>
+ Returns the number of elements in this sequence type.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD>Returns the number of elements in this sequence type.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIntForElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+getIntForElement</H3>
+<PRE>
+public int <B>getIntForElement</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD>This method is present as a performance enhancement. For every
+ Element this method should return a unique and repeatable int,
+ starting at 0 and ending at size() - 1 for all possible
+ Elements. This enables the Element to be used as an index for an
+ array which in turn allows implementation of efficient look up
+ tables, rather than using a hashtable.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>a int</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementForInt(int)"><!-- --></A><H3>
+getElementForInt</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementForInt</B>(int index)</PRE>
+<DL>
+<DD>The inverse of the method getIntForElement.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - a value of type 'int'
+<DT><B>Returns:</B><DD>a value of type 'Element'</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElements()"><!-- --></A><H3>
+getElements</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getElements</B>()</PRE>
+<DL>
+<DD>Returns all the elements available in this sequence type.
+ This array should be freely modifiable, and changes should not
+ percolate backwards iunto the internal data of the sequence
+ type.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD>Returns the human readable form of this sequence type.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char element)</PRE>
+<DL>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char[] elements)</PRE>
+<DL>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</PRE>
+<DL>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/Sequences.html b/doc/javadoc/uk/ac/man/bioinf/sequence/Sequences.html
new file mode 100644
index 0000000..6db03a9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/Sequences.html
@@ -0,0 +1,667 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+Sequences
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Sequences";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Sequences.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence</FONT>
+<BR>
+Class Sequences</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.Sequences</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Sequences</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Sequences.java
+
+
+ Created: Tue Mar 14 13:43:59 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Sequences.java,v 1.15 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#chompLeadingGaps(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">chompLeadingGaps</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ This removes all of the leading gaps from a gapped sequence, and
+ then returns the number of gaps removed.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#chompTrailingGaps(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">chompTrailingGaps</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ Removes and returns the number of trailing gaps off a gapped
+ sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getComplexSequenceAsString(uk.ac.man.bioinf.sequence.complex.ComplexSequence)">getComplexSequenceAsString</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)">getElementsAsGappedSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ Returns a GappedSequence with the Elements in the array, which
+ can included gaps.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">getElementsAsGappedSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ Returns a GappedSequence with the Elements in the array, which
+ can included gaps.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)">getElementsAsSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">getElementsAsSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getElementsAsString(uk.ac.man.bioinf.sequence.Element[])">getElementsAsString</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getGappedSequenceAsString(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getGappedSequenceAsString</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getGappedSubSequenceAsString(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int, int)">getGappedSubSequenceAsString</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int start,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getNumberGapsDownstreamFrom(int, uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getNumberGapsDownstreamFrom</A></B>(int index,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ Returns the number of gaps downstream from a given index in the
+ given sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getNumberGapsUpstreamFrom(int, uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getNumberGapsUpstreamFrom</A></B>(int index,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ Returns the number of gaps upstream from a given index in the
+ given sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getResiduesAsComplexElements(uk.ac.man.bioinf.sequence.Residue[])">getResiduesAsComplexElements</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] elements)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getSequenceAsString(uk.ac.man.bioinf.sequence.Sequence)">getSequenceAsString</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#getSubSequenceAsString(uk.ac.man.bioinf.sequence.Sequence, int, int)">getSubSequenceAsString</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ int start,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#printAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">printAlignment</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> align)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#printElements(uk.ac.man.bioinf.sequence.Element[])">printElements</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.complex.ComplexSequence)">printSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.complex.GappedComplexSequence)">printSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">printSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html#printSequence(uk.ac.man.bioinf.sequence.Sequence)">printSequence</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+getElementsAsGappedSequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getElementsAsGappedSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+<DD>Returns a GappedSequence with the Elements in the array, which
+ can included gaps. All other elements must be contained in the
+ SequenceType however.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements<DD><CODE>type</CODE> - the sequence type
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+getElementsAsGappedSequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getElementsAsGappedSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+<DD>Returns a GappedSequence with the Elements in the array, which
+ can included gaps. All other elements must be contained in the
+ SequenceType however.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements<DD><CODE>type</CODE> - the sequence type
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+getElementsAsSequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getElementsAsSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+getElementsAsSequence</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getElementsAsSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="chompLeadingGaps(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+chompLeadingGaps</H3>
+<PRE>
+public static int <B>chompLeadingGaps</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>This removes all of the leading gaps from a gapped sequence, and
+ then returns the number of gaps removed.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence to chomp
+<DT><B>Returns:</B><DD>the number of gaps
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="chompTrailingGaps(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+chompTrailingGaps</H3>
+<PRE>
+public static int <B>chompTrailingGaps</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)
+ throws <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Removes and returns the number of trailing gaps off a gapped
+ sequence.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence
+<DT><B>Returns:</B><DD>the number of gaps
+<DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberGapsUpstreamFrom(int, uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getNumberGapsUpstreamFrom</H3>
+<PRE>
+public static int <B>getNumberGapsUpstreamFrom</B>(int index,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD>Returns the number of gaps upstream from a given index in the
+ given sequence. If the index is out of bounds, it returns zero.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location in the sequence to start counting
+ upstream from<DD><CODE>seq</CODE> - the sequence
+<DT><B>Returns:</B><DD>the number of gaps upstream for the given location</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberGapsDownstreamFrom(int, uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getNumberGapsDownstreamFrom</H3>
+<PRE>
+public static int <B>getNumberGapsDownstreamFrom</B>(int index,
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD>Returns the number of gaps downstream from a given index in the
+ given sequence. If the index is out of bounds, it returns zero.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location in the sequence to start counting
+ downstream from<DD><CODE>seq</CODE> - the sequence
+<DT><B>Returns:</B><DD>the number of gaps downstream for the given location</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsString(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+getSequenceAsString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getSequenceAsString</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubSequenceAsString(uk.ac.man.bioinf.sequence.Sequence, int, int)"><!-- --></A><H3>
+getSubSequenceAsString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getSubSequenceAsString</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ int start,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsString(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getGappedSequenceAsString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getGappedSequenceAsString</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSubSequenceAsString(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int, int)"><!-- --></A><H3>
+getGappedSubSequenceAsString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getGappedSubSequenceAsString</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int start,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsString(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+getElementsAsString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getElementsAsString</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexSequenceAsString(uk.ac.man.bioinf.sequence.complex.ComplexSequence)"><!-- --></A><H3>
+getComplexSequenceAsString</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getComplexSequenceAsString</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getResiduesAsComplexElements(uk.ac.man.bioinf.sequence.Residue[])"><!-- --></A><H3>
+getResiduesAsComplexElements</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] <B>getResiduesAsComplexElements</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] elements)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+printAlignment</H3>
+<PRE>
+public static void <B>printAlignment</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> align)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+printSequence</H3>
+<PRE>
+public static void <B>printSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printSequence(uk.ac.man.bioinf.sequence.complex.ComplexSequence)"><!-- --></A><H3>
+printSequence</H3>
+<PRE>
+public static void <B>printSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printSequence(uk.ac.man.bioinf.sequence.complex.GappedComplexSequence)"><!-- --></A><H3>
+printSequence</H3>
+<PRE>
+public static void <B>printSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printSequence(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+printSequence</H3>
+<PRE>
+public static void <B>printSequence</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printElements(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+printElements</H3>
+<PRE>
+public static void <B>printElements</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Sequences.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html
new file mode 100644
index 0000000..3d74f6b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html
@@ -0,0 +1,563 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:26 BST 2002 -->
+<TITLE>
+AbstractGappedSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractGappedSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class AbstractGappedSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/Sequenc [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html">DefaultGappedSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractGappedSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></DL>
+
+<P>
+AbstractGappedSequence.java
+
+
+ Created: Sat Mar 4 12:17:02 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractGappedSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#AbstractGappedSequence(uk.ac.man.bioinf.sequence.SequenceType)">AbstractGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRange(int)">checkGappedRange</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRangeForInsert(int)">checkGappedRangeForInsert</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int)">deleteGapAt</A></B>(int index)</CODE>
+
+<BR>
+ Delete the element at index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Delete the elements starting at index for the specified length</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAtQuietly(int)">deleteGapAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#getGappedSequenceIndexException(int)">getGappedSequenceIndexException</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAt(int)">insertGapAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAt(int, int)">insertGapAt</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Inserts the elements at this position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAtQuietly(int)">insertGapAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequenc [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.GappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedLength()">getGappedLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedS [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/S [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractGappedSequence(uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+AbstractGappedSequence</H3>
+<PRE>
+public <B>AbstractGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="insertGapAtQuietly(int)"><!-- --></A><H3>
+insertGapAtQuietly</H3>
+<PRE>
+protected abstract void <B>insertGapAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int)">insertGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int, int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int index,
+ int length)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Inserts the elements at this position. If the index is one longer
+ than the length of the sequence the sequence will be extended.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int, int)">insertGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index at which to insert
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAtQuietly(int)"><!-- --></A><H3>
+deleteGapAtQuietly</H3>
+<PRE>
+protected abstract void <B>deleteGapAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Delete the element at index.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to delete
+<DT><B>Returns:</B><DD>the element which has just been deleted
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int, int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int index,
+ int length)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Delete the elements starting at index for the specified length
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to start at<DD><CODE>length</CODE> - the length to delete
+<DT><B>Returns:</B><DD>the elements just deleted
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAtAsChar(int)"><!-- --></A><H3>
+getGappedElementAtAsChar</H3>
+<PRE>
+public char <B>getGappedElementAtAsChar</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsChars()"><!-- --></A><H3>
+getGappedSequenceAsChars</H3>
+<PRE>
+public char[] <B>getGappedSequenceAsChars</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkGappedRange(int)"><!-- --></A><H3>
+checkGappedRange</H3>
+<PRE>
+protected void <B>checkGappedRange</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkGappedRangeForInsert(int)"><!-- --></A><H3>
+checkGappedRangeForInsert</H3>
+<PRE>
+protected void <B>checkGappedRangeForInsert</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceIndexException(int)"><!-- --></A><H3>
+getGappedSequenceIndexException</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A> <B>getGappedSequenceIndexException</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html
new file mode 100644
index 0000000..51c9383
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html
@@ -0,0 +1,807 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:26 BST 2002 -->
+<TITLE>
+AbstractSequenceAlignment
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequenceAlignment";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class AbstractSequenceAlignment</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF= [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequenceAlignment</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></DL>
+
+<P>
+AbstractSequenceAlignment.java
+
+ An abstract class to extend for the basic definition of a multiple
+ sequence alignment. This class basically ensures listener handling.
+
+ Created: Mon Feb 21 13:02:10 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequenceAlignment.java,v 1.13 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#AbstractSequenceAlignment()">AbstractSequenceAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Delegates to the AlignmentListenerSupport object, the addition
+ of a Multiple Sequence (MS) listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</CODE>
+
+<BR>
+ Adds a sequence to the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">addSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> align)</CODE>
+
+<BR>
+ Calls addSequence on every sequence in the supplied
+ alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequenceQuietly</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> sequence,
+ int inset)</CODE>
+
+<BR>
+ Adds a sequence to the alignment, quietly, without notifying
+ listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Delegates to the AlignmentListenerSupport the addition of a
+ vetoable MS listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#fireAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">fireAlignmentEvent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#fireVetoableAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)">fireVetoableAlignmentEvent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Delegates to the AlignmentListenerSupport the removal of the
+ MS listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequence(int)">removeSequence</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Removes a sequence from the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequenceQuietly(int)">removeSequenceQuietly</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Remove a sequence from the alignment, quietly, without notifying
+ listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Delegates to the AlignmentListenerSupport the removal of the
+ vetoable MS listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setInset(int, int)">setInset</A></B>(int seqIndex,
+ int inset)</CODE>
+
+<BR>
+ Set the inset (or number of preceeding gaps) in a sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setInsetQuietly(int, int)">setInsetQuietly</A></B>(int seqIndex,
+ int inset)</CODE>
+
+<BR>
+ Set the inset (or number of preceeding gaps) in a sequence, quietly
+ without notifying listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setLengthQuietly(int)">setLengthQuietly</A></B>(int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ Method signalled before a prospective change occurs</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.SequenceAlignment"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getInset(int)">getInset</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getNumberSequences()">getNumberSequences</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceAt(int)">getSequenceAt</ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequenceAlignment()"><!-- --></A><H3>
+AbstractSequenceAlignment</H3>
+<PRE>
+public <B>AbstractSequenceAlignment</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setLengthQuietly(int)"><!-- --></A><H3>
+setLengthQuietly</H3>
+<PRE>
+protected abstract void <B>setLengthQuietly</B>(int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+addSequenceQuietly</H3>
+<PRE>
+protected abstract void <B>addSequenceQuietly</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> sequence,
+ int inset)</PRE>
+<DL>
+<DD>Adds a sequence to the alignment, quietly, without notifying
+ listeners.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence<DD><CODE>inset</CODE> - the inset of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+addSequence</H3>
+<PRE>
+public void <B>addSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Adds a sequence to the alignment. This action can be vetoed by a
+ listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence<DD><CODE>inset</CODE> - the sequence inset
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE> - veto to the addition</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequence(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+addSequence</H3>
+<PRE>
+public void <B>addSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> align)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Calls addSequence on every sequence in the supplied
+ alignment. This basically provides a simple shortcut method.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>align</CODE> - the alignment of sequences to be added
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE> - veto to the addition - this can
+ be sequence based as well as alignment based</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceQuietly(int)"><!-- --></A><H3>
+removeSequenceQuietly</H3>
+<PRE>
+protected abstract <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>removeSequenceQuietly</B>(int seqIndex)</PRE>
+<DL>
+<DD>Remove a sequence from the alignment, quietly, without notifying
+ listeners.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequence(int)"><!-- --></A><H3>
+removeSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>removeSequence</B>(int seqIndex)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Removes a sequence from the alignment. This action can be veetoed
+ by a listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#removeSequence(int)">removeSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the sequence
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE> - veto to the removal</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInsetQuietly(int, int)"><!-- --></A><H3>
+setInsetQuietly</H3>
+<PRE>
+protected abstract void <B>setInsetQuietly</B>(int seqIndex,
+ int inset)</PRE>
+<DL>
+<DD>Set the inset (or number of preceeding gaps) in a sequence, quietly
+ without notifying listeners.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index<DD><CODE>inset</CODE> - the inset or preceeding number of gaps</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInset(int, int)"><!-- --></A><H3>
+setInset</H3>
+<PRE>
+public void <B>setInset</B>(int seqIndex,
+ int inset)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Set the inset (or number of preceeding gaps) in a sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#setInset(int, int)">setInset</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index<DD><CODE>inset</CODE> - the inset or preceeding number of gaps
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+fireAlignmentEvent</H3>
+<PRE>
+protected void <B>fireAlignmentEvent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireVetoableAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><!-- --></A><H3>
+fireVetoableAlignmentEvent</H3>
+<PRE>
+protected void <B>fireVetoableAlignmentEvent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Delegates to the AlignmentListenerSupport object, the addition
+ of a Multiple Sequence (MS) listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a MS listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Delegates to the AlignmentListenerSupport the removal of the
+ MS listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the MS listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Delegates to the AlignmentListenerSupport the addition of a
+ vetoable MS listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a vetoable MS listener to be added</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Delegates to the AlignmentListenerSupport the removal of the
+ vetoable MS listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable MS listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></B></DD>
+<DD>Method signalled before a prospective change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE> - if the listener does not wish
+ the event to occur.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html
new file mode 100644
index 0000000..06383c7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html
@@ -0,0 +1,363 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:27 BST 2002 -->
+<TITLE>
+AlignmentColumn
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentColumn";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentColumn.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class AlignmentColumn</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.AlignmentColumn</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignmentColumn</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AlignmentColumn.java
+
+ The Sequence and SequenceAlignment classes have been created to be fail-fast. They
+ throw exceptions if attempts are made to access and element outside
+ of the range of the sequence. Additionally the alignment allows
+ sequences to start at any place within the alignment which is very
+ nice, but has the disadvantage of being a little fiddly to use in some
+ circumstances. This class addresses this problem. Essentially it is
+ a mask over a sequence alignment. It can be moved to any column of
+ the alignment, and will then return the elements down that
+ column. It takes care of the offsets, and returns a simple gap
+ Element if a request is made for an Element from before a sequence
+ starts or after a sequence finishes, so long as the row > 0 and <
+ alignment.getLength().
+
+ Created: Wed Jun 7 14:23:43 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentColumn.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#AlignmentColumn()">AlignmentColumn</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#AlignmentColumn(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">AlignmentColumn</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#getAlignment()">getAlignment</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#getColumn()">getColumn</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#getElementAtRow(int)">getElementAtRow</A></B>(int row)</CODE>
+
+<BR>
+ Get the element for this column at the given row.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#setAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">setAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html#setColumn(int)">setColumn</A></B>(int column)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentColumn()"><!-- --></A><H3>
+AlignmentColumn</H3>
+<PRE>
+public <B>AlignmentColumn</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AlignmentColumn(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+AlignmentColumn</H3>
+<PRE>
+public <B>AlignmentColumn</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+setAlignment</H3>
+<PRE>
+public void <B>setAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAlignment()"><!-- --></A><H3>
+getAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getAlignment</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setColumn(int)"><!-- --></A><H3>
+setColumn</H3>
+<PRE>
+public void <B>setColumn</B>(int column)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getColumn()"><!-- --></A><H3>
+getColumn</H3>
+<PRE>
+public int <B>getColumn</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAtRow(int)"><!-- --></A><H3>
+getElementAtRow</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAtRow</B>(int row)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A>,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalStateException.html">IllegalStateException</A></PRE>
+<DL>
+<DD>Get the element for this column at the given row. This will
+ return a Gap element if in front or after the sequence.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>row</CODE> - the row
+<DT><B>Returns:</B><DD>the element
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A></CODE> - if row < 1 or row > getNumberSequences()
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalStateException.html">IllegalStateException</A></CODE> - if the alignment has not been set</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentColumn.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html
new file mode 100644
index 0000000..caa1a31
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html
@@ -0,0 +1,777 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:27 BST 2002 -->
+<TITLE>
+DefaultGappedSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultGappedSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class DefaultGappedSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/Sequenc [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultGappedSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></DL>
+
+<P>
+DefaultGappedSequence.java
+
+
+ Created: Sat Mar 4 12:28:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultGappedSequence.java,v 1.14 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#sequence">sequence</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#toGappedMap">toGappedMap</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)">DefaultGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ A new gapped sequence, with no gaps in it!</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.util.IntArrayList, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> toGappedMap,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#DefaultGappedSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.util.IntArrayList)">DefaultGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> toGappedMap)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#debugScreenDump()">debugScreenDump</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#deleteGapAtQuietly(int)">deleteGapAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)">getElementsAsGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">getElementsAsGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGapModelForElements(uk.ac.man.bioinf.sequence.Element[])">getGapModelForElements</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedLength()">getGappedLength</A></B>()</CODE>
+
+<BR>
+ Returns the gapped length of this sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></B>(int index)</CODE>
+
+<BR>
+ Translate between the gapped index, and the ungapped index</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></B>(int position,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></B>(int index)</CODE>
+
+<BR>
+ Translate between the gapped position and the ungapped
+ position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#insertGapAtQuietly(int)">insertGapAtQuietly</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html#stripGapsFromElements(uk.ac.man.bioinf.sequence.Element[], int)">stripGapsFromElements</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ int size)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRange(int)">checkGappedRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#checkGappedRangeForInsert(int)">checkGappedRangeForInsert</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Abs [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequenc [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="sequence"><!-- --></A><H3>
+sequence</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>sequence</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="toGappedMap"><!-- --></A><H3>
+toGappedMap</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> <B>toGappedMap</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultGappedSequence(uk.ac.man.bioinf.sequence.Sequence, uk.ac.man.bioinf.util.IntArrayList)"><!-- --></A><H3>
+DefaultGappedSequence</H3>
+<PRE>
+protected <B>DefaultGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq,
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> toGappedMap)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.util.IntArrayList, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultGappedSequence</H3>
+<PRE>
+protected <B>DefaultGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> toGappedMap,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultGappedSequence</H3>
+<PRE>
+public <B>DefaultGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+<DD>A new gapped sequence, with no gaps in it!
+<P>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - <DD><CODE>type</CODE> - </DL>
+<HR>
+
+<A NAME="DefaultGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultGappedSequence</H3>
+<PRE>
+public <B>DefaultGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="deleteGapAtQuietly(int)"><!-- --></A><H3>
+deleteGapAtQuietly</H3>
+<PRE>
+protected void <B>deleteGapAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#deleteGapAtQuietly(int)">deleteGapAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAtQuietly(int)"><!-- --></A><H3>
+insertGapAtQuietly</H3>
+<PRE>
+protected void <B>insertGapAtQuietly</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html#insertGapAtQuietly(int)">insertGapAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAt(int)"><!-- --></A><H3>
+getGappedElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getGappedElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsElements()"><!-- --></A><H3>
+getGappedSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getGappedSequenceAsElements</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedLength()"><!-- --></A><H3>
+getGappedLength</H3>
+<PRE>
+public int <B>getGappedLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Returns the gapped length of this sequence. That is the length of
+ the sequence including its gaps. Conversely this means that the
+ getLength method of the Sequence interface returns the length of
+ the sequence ignoring the gaps.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUngappedPositionOf(int)"><!-- --></A><H3>
+getUngappedPositionOf</H3>
+<PRE>
+public int <B>getUngappedPositionOf</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped position and the ungapped
+ position. I havent quite decided what to do at the moment if the
+ index refers to a gap. One idea is to throw a
+ NoSuchSequenceElementException which makes a certain amount of
+ sense but isnt really that useful. Perhaps a better idea is to
+ run -(insertion-point) where the insertion point is the nearest
+ element before the current requested position which is not a
+ gap. That way a value less than 0 would indicate a gap and would
+ also return a useful value
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedPositionOf(int)"><!-- --></A><H3>
+getGappedPositionOf</H3>
+<PRE>
+public int <B>getGappedPositionOf</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped index, and the ungapped index
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the ungapped position
+<DT><B>Returns:</B><DD>the gapped position of the equivalent element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSubSequence(int, int)"><!-- --></A><H3>
+getGappedSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getGappedSubSequence</B>(int position,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+getElementsAsGappedSequence</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getElementsAsGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+getElementsAsGappedSequence</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getElementsAsGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="stripGapsFromElements(uk.ac.man.bioinf.sequence.Element[], int)"><!-- --></A><H3>
+stripGapsFromElements</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] <B>stripGapsFromElements</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ int size)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGapModelForElements(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+getGapModelForElements</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> <B>getGapModelForElements</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="debugScreenDump()"><!-- --></A><H3>
+debugScreenDump</H3>
+<PRE>
+public void <B>debugScreenDump</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html
new file mode 100644
index 0000000..fdcb380
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html
@@ -0,0 +1,673 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:27 BST 2002 -->
+<TITLE>
+DefaultSequenceAlignment
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultSequenceAlignment";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class DefaultSequenceAlignment</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF= [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html">SingleSequenceAlignment</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultSequenceAlignment</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></DL>
+
+<P>
+DefaultSequenceAlignment.java
+
+ A class to model the multiple sequence alignment.
+ NB: Sequence numbering starts at 1 <b>NOT</b> 0.
+
+ Created: Mon Feb 21 13:51:11 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultSequenceAlignment.java,v 1.24 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.Element[][], uk.ac.man.bioinf.sequence.SequenceType)">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[][] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType)">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[])">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ int[] inset)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[], uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ int[] inset,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.SequenceType)">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.SequenceType)">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequenceQuietly</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</CODE>
+
+<BR>
+ Adds a sequence quietly to the alignment (i.e., without notifying
+ listeners - it should really only be done from it's parent
+ procedure addSequence).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getInset(int)">getInset</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Returns the inset of a particular sequence in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the multiple sequence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getNumberSequences()">getNumberSequences</A></B>()</CODE>
+
+<BR>
+ Returns the total number of sequences in the multiple sequence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSequenceAt(int)">getSequenceAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns the sequence, given a specific location in the MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceIndex</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ Returns the location of a sequence, in the multiple sequence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the sequence type for the alignment (e.g: Protien Sequence).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getSubAlignment(int, int, int, int)">getSubAlignment</A></B>(int startPos,
+ int length,
+ int startSeq,
+ int numSeqs)</CODE>
+
+<BR>
+ Returns a sub-alignment, given the exact location in this alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#init(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[], uk.ac.man.bioinf.sequence.identifier.Identifier)">init</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ int[] inset,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#removeSequenceQuietly(int)">removeSequenceQuietly</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Removes a sequence from the alignment, quietly, i.e., without
+ notifying any listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#setInsetQuietly(int, int)">setInsetQuietly</A></B>(int seqIndex,
+ int inset)</CODE>
+
+<BR>
+ Sets the inset (or preceeding number of gaps) for a sequence in the
+ alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#setLengthQuietly(int)">setLengthQuietly</A></B>(int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addS [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.Element[][], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[][] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[], uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ int[] inset,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[])"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ int[] inset)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+DefaultSequenceAlignment</H3>
+<PRE>
+public <B>DefaultSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="init(uk.ac.man.bioinf.sequence.alignment.GappedSequence[], uk.ac.man.bioinf.sequence.SequenceType, int[], uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+init</H3>
+<PRE>
+protected void <B>init</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] seqs,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ int[] inset,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> ident)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(int, int, int, int)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(int startPos,
+ int length,
+ int startSeq,
+ int numSeqs)</PRE>
+<DL>
+<DD>Returns a sub-alignment, given the exact location in this alignment.
+ NB: Sequencing numbering and alignment numbering start at 1 <b>NOT</b>
+ 0.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>startPos</CODE> - the start position for the sub-alignment (i.e: x1)<DD><CODE>length</CODE> - the length of the sub-alignment<DD><CODE>startSeq</CODE> - the first sequence in the current alignment to be
+ included in the sub-alignment (i.e: y1)<DD><CODE>numSeqs</CODE> - the number of sequences to be included in the
+ sub-alignment
+<DT><B>Returns:</B><DD>the sub-MSA</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD>Returns the sequence type for the alignment (e.g: Protien Sequence).
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAt(int)"><!-- --></A><H3>
+getSequenceAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSequenceAt</B>(int index)</PRE>
+<DL>
+<DD>Returns the sequence, given a specific location in the MSA.
+ NB: Alignment sequence numbering begins at 1 <b>NOT</b> 0.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location in the MSA of the target sequence
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getSequenceIndex</H3>
+<PRE>
+public int <B>getSequenceIndex</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD>Returns the location of a sequence, in the multiple sequence alignment.
+ NB:
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence of interest
+<DT><B>Returns:</B><DD>the location (-1 if sequence not found)</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setLengthQuietly(int)"><!-- --></A><H3>
+setLengthQuietly</H3>
+<PRE>
+protected void <B>setLengthQuietly</B>(int length)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setLengthQuietly(int)">setLengthQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+addSequenceQuietly</H3>
+<PRE>
+protected void <B>addSequenceQuietly</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</PRE>
+<DL>
+<DD>Adds a sequence quietly to the alignment (i.e., without notifying
+ listeners - it should really only be done from it's parent
+ procedure addSequence).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequenceQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence<DD><CODE>inset</CODE> - the sequence inset in the alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceQuietly(int)"><!-- --></A><H3>
+removeSequenceQuietly</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>removeSequenceQuietly</B>(int seqIndex)</PRE>
+<DL>
+<DD>Removes a sequence from the alignment, quietly, i.e., without
+ notifying any listeners. This procedure ought only to be called
+ from its "parent", removeSequence (unless you really know what
+ you are doing - hence the public nature of the function).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#removeSequenceQuietly(int)">removeSequenceQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the removed sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInsetQuietly(int, int)"><!-- --></A><H3>
+setInsetQuietly</H3>
+<PRE>
+protected void <B>setInsetQuietly</B>(int seqIndex,
+ int inset)</PRE>
+<DL>
+<DD>Sets the inset (or preceeding number of gaps) for a sequence in the
+ alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#setInsetQuietly(int, int)">setInsetQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index for the inset to be added to<DD><CODE>inset</CODE> - the inset</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInset(int)"><!-- --></A><H3>
+getInset</H3>
+<PRE>
+public int <B>getInset</B>(int seqIndex)</PRE>
+<DL>
+<DD>Returns the inset of a particular sequence in the alignment.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the inset</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSequences()"><!-- --></A><H3>
+getNumberSequences</H3>
+<PRE>
+public int <B>getNumberSequences</B>()</PRE>
+<DL>
+<DD>Returns the total number of sequences in the multiple sequence alignment.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the total number of sequences</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD>Returns the length of the multiple sequence alignment.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html
new file mode 100644
index 0000000..a50482d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html
@@ -0,0 +1,871 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:27 BST 2002 -->
+<TITLE>
+EmptyGappedSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="EmptyGappedSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptyGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class EmptyGappedSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/Sequenc [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>EmptyGappedSequence</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></DL>
+
+<P>
+EmptyGappedSequence.java
+
+
+ Created: Tue Nov 7 18:15:06 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: EmptyGappedSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> param1)</CODE>
+
+<BR>
+ Adds the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> param1)</CODE>
+
+<BR>
+ Adds the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#deleteGapAt(int)">deleteGapAt</A></B>(int param1)</CODE>
+
+<BR>
+ Delete the element at index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Delete the elements starting at index for the specified length</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getElementAt(int)">getElementAt</A></B>(int param1)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></B>(int param1)</CODE>
+
+<BR>
+ Returns the character of an target element.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A></B>(int param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></B>(int param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedLength()">getGappedLength</A></B>()</CODE>
+
+<BR>
+ Returns the gapped length of this sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></B>(int param1)</CODE>
+
+<BR>
+ Translate between the gapped index, and the ungapped index</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSequenceAsChars()">getSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of characters.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the type of sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getSubSequence(int, int)">getSubSequence</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Returns a sub-sequence from the current sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></B>(int param1)</CODE>
+
+<BR>
+ Translate between the gapped position and the ungapped
+ position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#insertGapAt(int)">insertGapAt</A></B>(int param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#insertGapAt(int, int)">insertGapAt</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Inserts the elements at this position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> param1)</CODE>
+
+<BR>
+ Removes the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> param1)</CODE>
+
+<BR>
+ Removes the specified vetoable sequence listener.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html">EmptyGappedSequence</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubSequence(int, int)"><!-- --></A><H3>
+getSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getSubSequence</B>(int param1,
+ int param2)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns a sub-sequence from the current sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the initial index of the sub-sequence
+<DT><B>Returns:</B><DD>the sub-sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the type of sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsChars()"><!-- --></A><H3>
+getSequenceAsChars</H3>
+<PRE>
+public char[] <B>getSequenceAsChars</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of characters.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAtAsChar(int)"><!-- --></A><H3>
+getElementAtAsChar</H3>
+<PRE>
+public char <B>getElementAtAsChar</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the character of an target element.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element character</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int, int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int param1,
+ int param2)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Inserts the elements at this position. If the index is one longer
+ than the length of the sequence the sequence will be extended.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int, int)">insertGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the index at which to insert
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the element does not
+ exist, which will be the case if index is less than 1 or greater
+ than sequence length + 1
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int param1)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int)">insertGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUngappedPositionOf(int)"><!-- --></A><H3>
+getUngappedPositionOf</H3>
+<PRE>
+public int <B>getUngappedPositionOf</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped position and the ungapped
+ position. I havent quite decided what to do at the moment if the
+ index refers to a gap. One idea is to throw a
+ NoSuchSequenceElementException which makes a certain amount of
+ sense but isnt really that useful. Perhaps a better idea is to
+ run -(insertion-point) where the insertion point is the nearest
+ element before the current requested position which is not a
+ gap. That way a value less than 0 would indicate a gap and would
+ also return a useful value
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSubSequence(int, int)"><!-- --></A><H3>
+getGappedSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getGappedSubSequence</B>(int param1,
+ int param2)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsElements()"><!-- --></A><H3>
+getGappedSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getGappedSequenceAsElements</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsChars()"><!-- --></A><H3>
+getGappedSequenceAsChars</H3>
+<PRE>
+public char[] <B>getGappedSequenceAsChars</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedPositionOf(int)"><!-- --></A><H3>
+getGappedPositionOf</H3>
+<PRE>
+public int <B>getGappedPositionOf</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped index, and the ungapped index
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the ungapped position
+<DT><B>Returns:</B><DD>the gapped position of the equivalent element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedLength()"><!-- --></A><H3>
+getGappedLength</H3>
+<PRE>
+public int <B>getGappedLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Returns the gapped length of this sequence. That is the length of
+ the sequence including its gaps. Conversely this means that the
+ getLength method of the Sequence interface returns the length of
+ the sequence ignoring the gaps.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedLength()">getGappedLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAtAsChar(int)"><!-- --></A><H3>
+getGappedElementAtAsChar</H3>
+<PRE>
+public char <B>getGappedElementAtAsChar</B>(int param1)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAt(int)"><!-- --></A><H3>
+getGappedElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getGappedElementAt</B>(int param1)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int, int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int param1,
+ int param2)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Delete the elements starting at index for the specified length
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the index to start at<DD><CODE>param2</CODE> - the length to delete
+<DT><B>Returns:</B><DD>the elements just deleted
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the elements do not all
+ exist, so if index is less than 1, or index + length is greater
+ than the length of the sequence
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int param1)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Delete the element at index.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the index to delete
+<DT><B>Returns:</B><DD>the element which has just been deleted
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if index is less than 1
+ or greater than the length of the sequence
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptyGappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html
new file mode 100644
index 0000000..b5e91ed
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html
@@ -0,0 +1,855 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:28 BST 2002 -->
+<TITLE>
+EmptySequenceAlignment
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="EmptySequenceAlignment";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptySequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class EmptySequenceAlignment</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF= [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>EmptySequenceAlignment</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></DL>
+
+<P>
+EmptySequenceAlignment.java
+
+
+ Created: Wed Apr 19 17:23:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: EmptySequenceAlignment.java,v 1.7 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Add a listener specifically interested in events connected with the MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</CODE>
+
+<BR>
+ Adds a sequence to the current alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a listener interested in vetoing multiple sequence alignment
+ specific events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getInset(int)">getInset</A></B>(int index)</CODE>
+
+<BR>
+ Returns the inset of sequence within the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the alignment (i.e: the longest sequence).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getNumberSequences()">getNumberSequences</A></B>()</CODE>
+
+<BR>
+ Returns the total number of sequences in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSequenceAt(int)">getSequenceAt</A></B>(int index)</CODE>
+
+<BR>
+ Provides the sequence at a particular location in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceIndex</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ Returns the index in the alignment of a provided sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the sequence type of the alignment (e.g: protein sequences).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSubAlignment(int, int, int, int)">getSubAlignment</A></B>(int a,
+ int b,
+ int c,
+ int d)</CODE>
+
+<BR>
+ Returns a sub-alignment, given the exact location in this alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeSequence(int)">removeSequence</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Removes a sequence from the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#setInset(int, int)">setInset</A></B>(int seqIndex,
+ int size)</CODE>
+
+<BR>
+ Sets the inset of a sequence within the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#setInsetQuietly(int, int)">setInsetQuietly</A></B>(int seqIndex,
+ int inset)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#setLengthQuietly(int)">setLengthQuietly</A></B>(int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ Method signalled before a prospective change occurs</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInset(int)"><!-- --></A><H3>
+getInset</H3>
+<PRE>
+public int <B>getInset</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the inset of sequence within the alignment.
+ A inset of 0 means that the first element means that the Sequence
+ starts at the left most position of the alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getInset(int)">getInset</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the inset or preceeding number of gaps</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the length of the alignment (i.e: the longest sequence).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>length of alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSequences()"><!-- --></A><H3>
+getNumberSequences</H3>
+<PRE>
+public int <B>getNumberSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the total number of sequences in the alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getNumberSequences()">getNumberSequences</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of sequences</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAt(int)"><!-- --></A><H3>
+getSequenceAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSequenceAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Provides the sequence at a particular location in the alignment.
+ The indexing STARTS AT 1, and not 0.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceAt(int)">getSequenceAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index of the target sequence
+<DT><B>Returns:</B><DD>the sequence of interest</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getSequenceIndex</H3>
+<PRE>
+public int <B>getSequenceIndex</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the index in the alignment of a provided sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceIndex</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the query sequence
+<DT><B>Returns:</B><DD>the index of the sequence, or -1 if not found</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the sequence type of the alignment (e.g: protein sequences).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceType()">getSequenceType</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(int, int, int, int)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(int a,
+ int b,
+ int c,
+ int d)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns a sub-alignment, given the exact location in this alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(int, int, int, int)">getSubAlignment</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>a</CODE> - the start position for the sub-alignment (i.e: x1)<DD><CODE>b</CODE> - the length of the sub alignment<DD><CODE>c</CODE> - the first sequence in the current alignment to be
+ included in the sub-alignment (i.e: y1)
+<DT><B>Returns:</B><DD>the sub-alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInset(int, int)"><!-- --></A><H3>
+setInset</H3>
+<PRE>
+public void <B>setInset</B>(int seqIndex,
+ int size)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Sets the inset of a sequence within the alignment. An inset of
+ zero will mean that the first element starts at the left most
+ position of the alignment.
+ <p>
+ Special N.B.: This was put into the interface because it was
+ felt that there would not be any instances when you would not
+ wish to do this (apart from a read-only alignment, in which case
+ there are ways and means).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#setInset(int, int)">setInset</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the index of the sequence<DD><CODE>size</CODE> - the size of the inset</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInsetQuietly(int, int)"><!-- --></A><H3>
+setInsetQuietly</H3>
+<PRE>
+public void <B>setInsetQuietly</B>(int seqIndex,
+ int inset)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+addSequence</H3>
+<PRE>
+public void <B>addSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Adds a sequence to the current alignment. If listeners are
+ listening to the alignment, they will be able to veto the add
+ (thats the idea atleast).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence to be added<DD><CODE>inset</CODE> - the sequence inset</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequence(int)"><!-- --></A><H3>
+removeSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>removeSequence</B>(int seqIndex)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Removes a sequence from the alignment. It requires the knowledge
+ of the sequence location in the alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#removeSequence(int)">removeSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the index of the sequence
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setLengthQuietly(int)"><!-- --></A><H3>
+setLengthQuietly</H3>
+<PRE>
+public void <B>setLengthQuietly</B>(int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Add a listener specifically interested in events connected with the MSA.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Adds a listener interested in vetoing multiple sequence alignment
+ specific events.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a vetoable multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a vetoable multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></B></DD>
+<DD>Method signalled before a prospective change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptySequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/Gap.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/Gap.html
new file mode 100644
index 0000000..a169af3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/Gap.html
@@ -0,0 +1,307 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+Gap
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Gap";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Gap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class Gap</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.Gap</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>Gap</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DL>
+
+<P>
+Gap.java
+
+
+ Created: Wed Mar 1 19:35:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Gap.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html#gap">gap</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html#GAP">GAP</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html#toChar()">toChar</A></B>()</CODE>
+
+<BR>
+ Returns a character representation of this element.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="gap"><!-- --></A><H3>
+gap</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A> <B>gap</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GAP"><!-- --></A><H3>
+GAP</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html">Gap</A> <B>GAP</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toChar()"><!-- --></A><H3>
+toChar</H3>
+<PRE>
+public char <B>toChar</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></B></DD>
+<DD>Returns a character representation of this element. This may be
+ non-alphanumeric, and should be unique within a SequenceType.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the char representation<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><CODE>SequenceType</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Gap.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/GappedSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/GappedSequence.html
new file mode 100644
index 0000000..54c8d1c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/GappedSequence.html
@@ -0,0 +1,556 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:25 BST 2002 -->
+<TITLE>
+GappedSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappedSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Interface GappedSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGap [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>GappedSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A></DL>
+
+<P>
+GappedSequence.java
+
+
+ Created: Wed Mar 1 18:28:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappedSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A></B>(int index)</CODE>
+
+<BR>
+ Delete the element at index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Delete the elements starting at index for the specified length</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A></B>(int position)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></B>(int position)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedLength()">getGappedLength</A></B>()</CODE>
+
+<BR>
+ Returns the gapped length of this sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></B>(int index)</CODE>
+
+<BR>
+ Translate between the gapped index, and the ungapped index</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></B>(int from,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></B>(int index)</CODE>
+
+<BR>
+ Translate between the gapped position and the ungapped
+ position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int)">insertGapAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int, int)">insertGapAt</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ Inserts the elements at this position.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/S [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getGappedSubSequence(int, int)"><!-- --></A><H3>
+getGappedSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getGappedSubSequence</B>(int from,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAt(int)"><!-- --></A><H3>
+getGappedElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getGappedElementAt</B>(int position)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAtAsChar(int)"><!-- --></A><H3>
+getGappedElementAtAsChar</H3>
+<PRE>
+public char <B>getGappedElementAtAsChar</B>(int position)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsElements()"><!-- --></A><H3>
+getGappedSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getGappedSequenceAsElements</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsChars()"><!-- --></A><H3>
+getGappedSequenceAsChars</H3>
+<PRE>
+public char[] <B>getGappedSequenceAsChars</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedLength()"><!-- --></A><H3>
+getGappedLength</H3>
+<PRE>
+public int <B>getGappedLength</B>()</PRE>
+<DL>
+<DD>Returns the gapped length of this sequence. That is the length of
+ the sequence including its gaps. Conversely this means that the
+ getLength method of the Sequence interface returns the length of
+ the sequence ignoring the gaps.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedPositionOf(int)"><!-- --></A><H3>
+getGappedPositionOf</H3>
+<PRE>
+public int <B>getGappedPositionOf</B>(int index)</PRE>
+<DL>
+<DD>Translate between the gapped index, and the ungapped index
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the ungapped position
+<DT><B>Returns:</B><DD>the gapped position of the equivalent element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUngappedPositionOf(int)"><!-- --></A><H3>
+getUngappedPositionOf</H3>
+<PRE>
+public int <B>getUngappedPositionOf</B>(int index)</PRE>
+<DL>
+<DD>Translate between the gapped position and the ungapped
+ position. I havent quite decided what to do at the moment if the
+ index refers to a gap. One idea is to throw a
+ NoSuchSequenceElementException which makes a certain amount of
+ sense but isnt really that useful. Perhaps a better idea is to
+ run -(insertion-point) where the insertion point is the nearest
+ element before the current requested position which is not a
+ gap. That way a value less than 0 would indicate a gap and would
+ also return a useful value
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int, int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int index,
+ int length)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Inserts the elements at this position. If the index is one longer
+ than the length of the sequence the sequence will be extended.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index at which to insert
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the element does not
+ exist, which will be the case if index is less than 1 or greater
+ than sequence length + 1
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Delete the element at index.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to delete
+<DT><B>Returns:</B><DD>the element which has just been deleted
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if index is less than 1
+ or greater than the length of the sequence
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int, int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int index,
+ int length)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Delete the elements starting at index for the specified length
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index to start at<DD><CODE>length</CODE> - the length to delete
+<DT><B>Returns:</B><DD>the elements just deleted
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE> - if the elements do not all
+ exist, so if index is less than 1, or index + length is greater
+ than the length of the sequence
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html
new file mode 100644
index 0000000..35d8bb3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html
@@ -0,0 +1,328 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+NoGapAtThisPositionException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoGapAtThisPositionException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoGapAtThisPositionException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class NoGapAtThisPositionException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoGapAtThisPositionException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+NoGapAtThisPositionException.java
+
+
+ Created: Sat Mar 4 14:04:07 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoGapAtThisPositionException.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#NoGapAtThisPositionException(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">NoGapAtThisPositionException</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> source,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#NoGapAtThisPositionException(java.lang.String)">NoGapAtThisPositionException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#NoGapAtThisPositionException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">NoGapAtThisPositionException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> source,
+ int index)</CODE>
+
+<BR>
+ Creates an object signalling an exception for no gap at a
+ particular position.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#getIndex()">getIndex</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html#getSource()">getSource</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoGapAtThisPositionException(java.lang.String)"><!-- --></A><H3>
+NoGapAtThisPositionException</H3>
+<PRE>
+public <B>NoGapAtThisPositionException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoGapAtThisPositionException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+NoGapAtThisPositionException</H3>
+<PRE>
+public <B>NoGapAtThisPositionException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> source,
+ int index)</PRE>
+<DL>
+<DD>Creates an object signalling an exception for no gap at a
+ particular position. This constructor stores the source and index
+ within the source where the exception was raised.
+<P>
+<DT><B>Parameters:</B><DD><CODE>message</CODE> - the message to use<DD><CODE>source</CODE> - the gapped sequence or source<DD><CODE>index</CODE> - the index in the source of the raised</DL>
+<HR>
+
+<A NAME="NoGapAtThisPositionException(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+NoGapAtThisPositionException</H3>
+<PRE>
+public <B>NoGapAtThisPositionException</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> source,
+ int index)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSource()"><!-- --></A><H3>
+getSource</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSource</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIndex()"><!-- --></A><H3>
+getIndex</H3>
+<PRE>
+public int <B>getIndex</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoGapAtThisPositionException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html
new file mode 100644
index 0000000..81a4203
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html
@@ -0,0 +1,287 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+NoSuchSequenceException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoSuchSequenceException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchSequenceException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class NoSuchSequenceException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoSuchSequenceException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+NoSuchSequenceException.java
+
+ Alerts to an invalid sequence index within a sequence alignment.
+
+ Created: Fri Mar 3 12:22:15 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoSuchSequenceException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException()">NoSuchSequenceException</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)">NoSuchSequenceException</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException(java.lang.String)">NoSuchSequenceException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html#NoSuchSequenceException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)">NoSuchSequenceException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoSuchSequenceException()"><!-- --></A><H3>
+NoSuchSequenceException</H3>
+<PRE>
+public <B>NoSuchSequenceException</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoSuchSequenceException(java.lang.String)"><!-- --></A><H3>
+NoSuchSequenceException</H3>
+<PRE>
+public <B>NoSuchSequenceException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoSuchSequenceException(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)"><!-- --></A><H3>
+NoSuchSequenceException</H3>
+<PRE>
+public <B>NoSuchSequenceException</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa,
+ int index)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoSuchSequenceException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, int)"><!-- --></A><H3>
+NoSuchSequenceException</H3>
+<PRE>
+public <B>NoSuchSequenceException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> msa,
+ int index)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchSequenceException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html
new file mode 100644
index 0000000..e3f6ead
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html
@@ -0,0 +1,554 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:26 BST 2002 -->
+<TITLE>
+SequenceAlignment
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignment";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Interface SequenceAlignment</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>, <A HREF=".. [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceAlignment</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiabl [...]
+
+<P>
+SequenceAlignment.java
+
+ This interface is designed to mimic a biological sequence alignment.
+ As a consequence, the sequences contained within should be
+ GappedSequence.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignment.java,v 1.17 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><CODE>Created: Tue Feb 15 16:24:23 2000</CODE></A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</CODE>
+
+<BR>
+ Adds a sequence to the current alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getInset(int)">getInset</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Returns the inset of sequence within the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the alignment (i.e: the longest sequence).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getNumberSequences()">getNumberSequences</A></B>()</CODE>
+
+<BR>
+ Returns the total number of sequences in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceAt(int)">getSequenceAt</A></B>(int index)</CODE>
+
+<BR>
+ Provides the sequence at a particular location in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceIndex</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ Returns the index in the alignment of a provided sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the sequence type of the alignment (e.g: protein sequences).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(int, int, int, int)">getSubAlignment</A></B>(int startPos,
+ int length,
+ int startSeq,
+ int numSeqs)</CODE>
+
+<BR>
+ Returns a sub-alignment, given the exact location in this alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#removeSequence(int)">removeSequence</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Removes a sequence from the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#setInset(int, int)">setInset</A></B>(int seqIndex,
+ int size)</CODE>
+
+<BR>
+ Sets the inset of a sequence within the alignment.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.VetoableSequenceListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/se [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSubAlignment(int, int, int, int)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(int startPos,
+ int length,
+ int startSeq,
+ int numSeqs)</PRE>
+<DL>
+<DD>Returns a sub-alignment, given the exact location in this alignment.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>startPos</CODE> - the start position for the sub-alignment (i.e: x1)<DD><CODE>length</CODE> - the length of the sub alignment<DD><CODE>startSeq</CODE> - the first sequence in the current alignment to be
+ included in the sub-alignment (i.e: y1)
+<DT><B>Returns:</B><DD>the sub-alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+addSequence</H3>
+<PRE>
+public void <B>addSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Adds a sequence to the current alignment. If listeners are
+ listening to the alignment, they will be able to veto the add
+ (thats the idea atleast).
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence to be added<DD><CODE>inset</CODE> - the sequence inset
+<DT><B>Throws:</B>
+<DD><CODE>veto</CODE> - to the addition
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequence(int)"><!-- --></A><H3>
+removeSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>removeSequence</B>(int seqIndex)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Removes a sequence from the alignment. It requires the knowledge
+ of the sequence location in the alignment.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the index of the sequence
+<DT><B>Returns:</B><DD>the sequence
+<DT><B>Throws:</B>
+<DD><CODE>veto</CODE> - to the removal
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInset(int, int)"><!-- --></A><H3>
+setInset</H3>
+<PRE>
+public void <B>setInset</B>(int seqIndex,
+ int size)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Sets the inset of a sequence within the alignment. An inset of
+ zero will mean that the first element starts at the left most
+ position of the alignment.
+ <p>
+ Special N.B.: This was put into the interface because it was
+ felt that there would not be any instances when you would not
+ wish to do this (apart from a read-only alignment, in which case
+ there are ways and means).
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the index of the sequence<DD><CODE>size</CODE> - the size of the inset
+<DT><B>Throws:</B>
+<DD><CODE>veto</CODE> - to setting
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInset(int)"><!-- --></A><H3>
+getInset</H3>
+<PRE>
+public int <B>getInset</B>(int seqIndex)</PRE>
+<DL>
+<DD>Returns the inset of sequence within the alignment.
+ A inset of 0 means that the first element means that the Sequence
+ starts at the left most position of the alignment
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the inset or preceeding number of gaps</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD>Returns the sequence type of the alignment (e.g: protein sequences).
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAt(int)"><!-- --></A><H3>
+getSequenceAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSequenceAt</B>(int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A></PRE>
+<DL>
+<DD>Provides the sequence at a particular location in the alignment.
+ The indexing STARTS AT 1, and not 0.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index of the target sequence
+<DT><B>Returns:</B><DD>the sequence of interest
+<DT><B>Throws:</B>
+<DD><CODE>if</CODE> - index < 1 or index > getNumberSequences()
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html">NoSuchSequenceException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getSequenceIndex</H3>
+<PRE>
+public int <B>getSequenceIndex</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD>Returns the index in the alignment of a provided sequence.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the query sequence
+<DT><B>Returns:</B><DD>the index of the sequence, or -1 if not found</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSequences()"><!-- --></A><H3>
+getNumberSequences</H3>
+<PRE>
+public int <B>getNumberSequences</B>()</PRE>
+<DL>
+<DD>Returns the total number of sequences in the alignment.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of sequences</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD>Returns the length of the alignment (i.e: the longest sequence).
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>length of alignment</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html
new file mode 100644
index 0000000..d2b5bfc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+SingleSequenceAlignment
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SingleSequenceAlignment";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment</FONT>
+<BR>
+Class SingleSequenceAlignment</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF= [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SingleSequenceAlignment</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A></DL>
+
+<P>
+SingleSequenceAlignment.java
+
+ This class is for those stick occasions when you want a
+ SequenceAlignment but all you have is a Sequence. I don't know how
+ to make an array all within a single line so I have had to make a
+ factory method here.
+
+ Created: Tue Aug 1 16:16:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SingleSequenceAlignment.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html#SingleSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">SingleSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html#getNumberOfSequences()">getNumberOfSequences</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html#getSingleSequence()">getSingleSequence</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html">DefaultSequenceAlignment</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#addSequenceQuietly(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequenceQuietly</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getIdentifier()">getIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html#getInset(int)">getInset</A>, <A HREF="../../../../../../uk/ac/man/ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.AbstractSequenceAlignment"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html#addS [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SingleSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+SingleSequenceAlignment</H3>
+<PRE>
+public <B>SingleSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getNumberOfSequences()"><!-- --></A><H3>
+getNumberOfSequences</H3>
+<PRE>
+public int <B>getNumberOfSequences</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSingleSequence()"><!-- --></A><H3>
+getSingleSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSingleSequence</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingleSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html
new file mode 100644
index 0000000..53090fe
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html
@@ -0,0 +1,363 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+AlignmentEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Class AlignmentEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignmentEvent</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></DL>
+
+<P>
+AlignmentEvent.java
+
+ Instances of this class represent an event to a MSA. It includes
+ reference to the location of the event, as well as its type.
+
+ Created: Tue Feb 15 19:57:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentEvent.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#AlignmentEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)">AlignmentEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</CODE>
+
+<BR>
+ Constructor to set the event source, location and type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#AlignmentEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)">AlignmentEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int end,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</CODE>
+
+<BR>
+ Constructor to set the event source, location and type.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getEnd()">getEnd</A></B>()</CODE>
+
+<BR>
+ Returns the end location of the event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getStart()">getStart</A></B>()</CODE>
+
+<BR>
+ Returns the start location of the event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getType()">getType</A></B>()</CODE>
+
+<BR>
+ Returns the multiple sequence event type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><!-- --></A><H3>
+AlignmentEvent</H3>
+<PRE>
+public <B>AlignmentEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</PRE>
+<DL>
+<DD>Constructor to set the event source, location and type.
+<P>
+<DT><B>Parameters:</B><DD><CODE>src</CODE> - the source of the event (i.e: the MSA)<DD><CODE>location</CODE> - the location of the event, or zero if not known<DD><CODE>type</CODE> - the multiple sequence event type</DL>
+<HR>
+
+<A NAME="AlignmentEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><!-- --></A><H3>
+AlignmentEvent</H3>
+<PRE>
+public <B>AlignmentEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int end,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</PRE>
+<DL>
+<DD>Constructor to set the event source, location and type. The location
+ is split into a start and end location.
+<P>
+<DT><B>Parameters:</B><DD><CODE>src</CODE> - the source of the event (i.e: the MSA)<DD><CODE>start</CODE> - the start location of the event<DD><CODE>end</CODE> - the end location of the event<DD><CODE>type</CODE> - the multiple sequence event type</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getStart()"><!-- --></A><H3>
+getStart</H3>
+<PRE>
+public int <B>getStart</B>()</PRE>
+<DL>
+<DD>Returns the start location of the event.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the start</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getEnd()"><!-- --></A><H3>
+getEnd</H3>
+<PRE>
+public int <B>getEnd</B>()</PRE>
+<DL>
+<DD>Returns the end location of the event.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the end</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getType()"><!-- --></A><H3>
+getType</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>getType</B>()</PRE>
+<DL>
+<DD>Returns the multiple sequence event type.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the event type</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html
new file mode 100644
index 0000000..703a3de
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html
@@ -0,0 +1,284 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+AlignmentEventProvider
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentEventProvider";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentEventProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Interface AlignmentEventProvider</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/CinemaModule.html">CinemaModule</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignme [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentEventProvider</B></DL>
+
+<P>
+AlignmentEventProvider.java
+
+
+ Created: Mon Apr 24 16:59:55 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentEventProvider.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Add a listener specifically interested in events connected with the MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a listener interested in vetoing multiple sequence alignment
+ specific events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable multiple sequence alignment listener.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Add a listener specifically interested in events connected with the MSA.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Removes a multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Adds a listener interested in vetoing multiple sequence alignment
+ specific events.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a vetoable multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Removes a vetoable multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentEventProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html
new file mode 100644
index 0000000..000e8b9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html
@@ -0,0 +1,353 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+AlignmentEventType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentEventType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentEventType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Class AlignmentEventType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType</B>
+</PRE>
+<HR>
+<DL>
+<DT>public final class <B>AlignmentEventType</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AlignmentEventType.java
+
+ This class provides an enumerated type for the AlignmentEvent class
+ to pass around as an identifier
+
+ Created: Tue Feb 15 20:26:54 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentEventType.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#DELETE">DELETE</A></B></CODE>
+
+<BR>
+ Event type indicated a sequence has been removed from the
+ sequence alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#INSERT">INSERT</A></B></CODE>
+
+<BR>
+ Event type indicating a new sequence has been added to the
+ sequence alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#INSET_CHANGE">INSET_CHANGE</A></B></CODE>
+
+<BR>
+ Event type indicating a change in the inset/preceeding number of gaps</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#LENGTH_CHANGE">LENGTH_CHANGE</A></B></CODE>
+
+<BR>
+ Event type indicating that the length of the alignment has
+ changed.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#UNSPECIFIED">UNSPECIFIED</A></B></CODE>
+
+<BR>
+ This type says that the alignment has changed in some unknown
+ way.</TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="INSERT"><!-- --></A><H3>
+INSERT</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>INSERT</B></PRE>
+<DL>
+<DD>Event type indicating a new sequence has been added to the
+ sequence alignment
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="DELETE"><!-- --></A><H3>
+DELETE</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>DELETE</B></PRE>
+<DL>
+<DD>Event type indicated a sequence has been removed from the
+ sequence alignment
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="INSET_CHANGE"><!-- --></A><H3>
+INSET_CHANGE</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>INSET_CHANGE</B></PRE>
+<DL>
+<DD>Event type indicating a change in the inset/preceeding number of gaps
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="LENGTH_CHANGE"><!-- --></A><H3>
+LENGTH_CHANGE</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>LENGTH_CHANGE</B></PRE>
+<DL>
+<DD>Event type indicating that the length of the alignment has
+ changed.
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="UNSPECIFIED"><!-- --></A><H3>
+UNSPECIFIED</H3>
+<PRE>
+public static final <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> <B>UNSPECIFIED</B></PRE>
+<DL>
+<DD>This type says that the alignment has changed in some unknown
+ way. This is very useful when its hard to work out what has
+ changed. Its probably going to be fairly inefficient as well, and
+ should be removed when feasible so that optimisations are possible.
+<P>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentEventType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html
new file mode 100644
index 0000000..d3cef20
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html
@@ -0,0 +1,225 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+AlignmentListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Interface AlignmentListener</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.html">CinemaCoreView</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.html">CinemaGroupFrame</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.html">CinemaGroupModule</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercenta [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>AlignmentListener</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DL>
+
+<P>
+AlignmentListener.java
+
+ Objects of this type should be signalled after a change has occured
+ to a multiple sequence alignment
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentListener.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><CODE>Created: Tue Feb 15 19:51:22 2000</CODE></A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html
new file mode 100644
index 0000000..2271b9f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html
@@ -0,0 +1,368 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+AlignmentListenerSupport
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentListenerSupport";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Class AlignmentListenerSupport</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>AlignmentListenerSupport</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AlignmentListenerSupport.java
+
+ This class provides support and handles the listeners to a multiple
+ seqyence alignment.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentListenerSupport.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><CODE>Created: Thu Feb 17 14:57:37 2000</CODE></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#AlignmentListenerSupport()">AlignmentListenerSupport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a alignment listener to a Vector of listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a vetoable alignment listener to the Vector of vetoable
+ listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#fireAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">fireAlignmentEvent</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ This function fires the MSA event to all the interested listeners, and also
+ signals the vetoable listeners, which are stored separately.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#fireVetoableAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)">fireVetoableAlignmentEvent</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)</CODE>
+
+<BR>
+ Notifies the vetoable listeners of a MSA vetoable event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a listener from the Vector.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable alignment listener.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentListenerSupport()"><!-- --></A><H3>
+AlignmentListenerSupport</H3>
+<PRE>
+public <B>AlignmentListenerSupport</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="fireAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+fireAlignmentEvent</H3>
+<PRE>
+public void <B>fireAlignmentEvent</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD>This function fires the MSA event to all the interested listeners, and also
+ signals the vetoable listeners, which are stored separately. This is
+ because the VetoableMultipleSequenceListener interface extends the
+ MultipleSequenceListener interface.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the multiple sequence event<DT><B>See Also:</B><DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><CODE>VetoableAlignmentListener</CODE></A>,
+<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><CODE>AlignmentListener</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireVetoableAlignmentEvent(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><!-- --></A><H3>
+fireVetoableAlignmentEvent</H3>
+<PRE>
+public void <B>fireVetoableAlignmentEvent</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Notifies the vetoable listeners of a MSA vetoable event.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the vetoable multiple sequence event
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Adds a alignment listener to a Vector of listeners.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be added</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Removes a listener from the Vector.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Adds a vetoable alignment listener to the Vector of vetoable
+ listeners.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable listener to be added.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD>Removes a vetoable alignment listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html
new file mode 100644
index 0000000..eb38873
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html
@@ -0,0 +1,276 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+AlignmentVetoException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AlignmentVetoException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentVetoException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Class AlignmentVetoException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AlignmentVetoException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A></DL>
+
+<P>
+AlignmentVetoExcception.java
+
+ An exception thrown when an object vetos an alignment event.
+
+ Created: Tue Feb 15 21:16:35 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AlignmentVetoException.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html#AlignmentVetoException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">AlignmentVetoException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ Constructor; includes reference to the event which spawned the veto.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html#getEvent()">getEvent</A></B>()</CODE>
+
+<BR>
+ Returns the multiple sequence event that spawned the veto.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AlignmentVetoException(java.lang.String, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+AlignmentVetoException</H3>
+<PRE>
+public <B>AlignmentVetoException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD>Constructor; includes reference to the event which spawned the veto.
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getEvent()"><!-- --></A><H3>
+getEvent</H3>
+<PRE>
+public <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> <B>getEvent</B>()</PRE>
+<DL>
+<DD>Returns the multiple sequence event that spawned the veto.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the event</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AlignmentVetoException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html
new file mode 100644
index 0000000..4feda8c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+VetoableAlignmentEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VetoableAlignmentEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableAlignmentEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Class VetoableAlignmentEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>VetoableAlignmentEvent</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A></DL>
+
+<P>
+VetoableAlignmentEvent.java
+
+ An event that may be vetoed by a listener.
+
+ Created: Fri Feb 18 17:41:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VetoableAlignmentEvent.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html#VetoableAlignmentEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)">VetoableAlignmentEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html#VetoableAlignmentEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)">VetoableAlignmentEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int end,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getEnd()">getEnd</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getStart()">getStart</A>, <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html#getType()">getType</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="VetoableAlignmentEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><!-- --></A><H3>
+VetoableAlignmentEvent</H3>
+<PRE>
+public <B>VetoableAlignmentEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="VetoableAlignmentEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType)"><!-- --></A><H3>
+VetoableAlignmentEvent</H3>
+<PRE>
+public <B>VetoableAlignmentEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int end,
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html">AlignmentEventType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableAlignmentEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html
new file mode 100644
index 0000000..3473937
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:29 BST 2002 -->
+<TITLE>
+VetoableAlignmentListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VetoableAlignmentListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableAlignmentListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.alignment.event</FONT>
+<BR>
+Interface VetoableAlignmentListener</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html">SequenceAlignmentTest</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>VetoableAlignmentListener</B><DT>extends <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></DL>
+
+<P>
+VetoableAlignmentListener.java
+
+ Listeners of this type are informed before a change takes place,
+ and throw an exception if they so wish. Following this a second
+ event is signalled to listeners of type AlignmentListener after
+ the change has occured. Because two events are signalled it
+ is not necessary to signal all VetoableAlignmentListener that a
+ change has not occured.
+
+ Created: Tue Feb 15 20:06:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VetoableAlignmentListener.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)</CODE>
+
+<BR>
+ Method called before a change occurs to an alignment</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)
+ throws <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD>Method called before a change occurs to an alignment
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> -
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableAlignmentListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-frame.html
new file mode 100644
index 0000000..7aeedb4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-frame.html
@@ -0,0 +1,64 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.alignment.event()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.alignment.event()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.alignment.event</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentEventProvider.html" TARGET="classFrame"><I>AlignmentEventProvider</I></A>
+<BR>
+<A HREF="AlignmentListener.html" TARGET="classFrame"><I>AlignmentListener</I></A>
+<BR>
+<A HREF="VetoableAlignmentListener.html" TARGET="classFrame"><I>VetoableAlignmentListener</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentEvent.html" TARGET="classFrame">AlignmentEvent</A>
+<BR>
+<A HREF="AlignmentEventType.html" TARGET="classFrame">AlignmentEventType</A>
+<BR>
+<A HREF="AlignmentListenerSupport.html" TARGET="classFrame">AlignmentListenerSupport</A>
+<BR>
+<A HREF="VetoableAlignmentEvent.html" TARGET="classFrame">VetoableAlignmentEvent</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AlignmentVetoException.html" TARGET="classFrame">AlignmentVetoException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-summary.html
new file mode 100644
index 0000000..1cbc459
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-summary.html
@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.alignment.event()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.alignment.event()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/complex/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.alignment.event
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentEventProvider.html"><I>AlignmentEventProvider</I></A></B></TD>
+<TD>AlignmentEventProvider.java
+
+
+ Created: Mon Apr 24 16:59:55 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentListener.html"><I>AlignmentListener</I></A></B></TD>
+<TD>AlignmentListener.java
+
+ Objects of this type should be signalled after a change has occured
+ to a multiple sequence alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VetoableAlignmentListener.html"><I>VetoableAlignmentListener</I></A></B></TD>
+<TD>VetoableAlignmentListener.java
+
+ Listeners of this type are informed before a change takes place,
+ and throw an exception if they so wish.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentEvent.html">AlignmentEvent</A></B></TD>
+<TD>AlignmentEvent.java
+
+ Instances of this class represent an event to a MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentEventType.html">AlignmentEventType</A></B></TD>
+<TD>AlignmentEventType.java
+
+ This class provides an enumerated type for the AlignmentEvent class
+ to pass around as an identifier
+
+ Created: Tue Feb 15 20:26:54 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentListenerSupport.html">AlignmentListenerSupport</A></B></TD>
+<TD>AlignmentListenerSupport.java
+
+ This class provides support and handles the listeners to a multiple
+ seqyence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VetoableAlignmentEvent.html">VetoableAlignmentEvent</A></B></TD>
+<TD>VetoableAlignmentEvent.java
+
+ An event that may be vetoed by a listener.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentVetoException.html">AlignmentVetoException</A></B></TD>
+<TD>AlignmentVetoExcception.java
+
+ An exception thrown when an object vetos an alignment event.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/complex/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-tree.html
new file mode 100644
index 0000000..0a896ae
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/event/package-tree.html
@@ -0,0 +1,151 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.alignment.event Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.alignment.event Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/complex/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.alignment.event
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.html"><B>AlignmentEventType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.html"><B>AlignmentListenerSupport</B></A><LI TYPE="circle">class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/ut [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html"><B>AlignmentEvent</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html"><B>VetoableAlignmentEvent</B></A></UL>
+</UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html"><B>AlignmentVetoException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html"><B>AlignmentEventProvider</B></A><LI TYPE="circle">interface java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html"><B>EventListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html"><B>AlignmentListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html"><B>VetoableAlignmentListener</B></A></UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/alignment/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../../uk/ac/man/bioinf/sequence/complex/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-frame.html
new file mode 100644
index 0000000..8094346
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-frame.html
@@ -0,0 +1,74 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.alignment()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.alignment()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.alignment</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="GappedSequence.html" TARGET="classFrame"><I>GappedSequence</I></A>
+<BR>
+<A HREF="SequenceAlignment.html" TARGET="classFrame"><I>SequenceAlignment</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractGappedSequence.html" TARGET="classFrame">AbstractGappedSequence</A>
+<BR>
+<A HREF="AbstractSequenceAlignment.html" TARGET="classFrame">AbstractSequenceAlignment</A>
+<BR>
+<A HREF="AlignmentColumn.html" TARGET="classFrame">AlignmentColumn</A>
+<BR>
+<A HREF="DefaultGappedSequence.html" TARGET="classFrame">DefaultGappedSequence</A>
+<BR>
+<A HREF="DefaultSequenceAlignment.html" TARGET="classFrame">DefaultSequenceAlignment</A>
+<BR>
+<A HREF="EmptyGappedSequence.html" TARGET="classFrame">EmptyGappedSequence</A>
+<BR>
+<A HREF="EmptySequenceAlignment.html" TARGET="classFrame">EmptySequenceAlignment</A>
+<BR>
+<A HREF="Gap.html" TARGET="classFrame">Gap</A>
+<BR>
+<A HREF="SingleSequenceAlignment.html" TARGET="classFrame">SingleSequenceAlignment</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="NoGapAtThisPositionException.html" TARGET="classFrame">NoGapAtThisPositionException</A>
+<BR>
+<A HREF="NoSuchSequenceException.html" TARGET="classFrame">NoSuchSequenceException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-summary.html
new file mode 100644
index 0000000..589c98e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-summary.html
@@ -0,0 +1,237 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.alignment()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.alignment()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.alignment
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappedSequence.html"><I>GappedSequence</I></A></B></TD>
+<TD>GappedSequence.java
+
+
+ Created: Wed Mar 1 18:28:44 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignment.html"><I>SequenceAlignment</I></A></B></TD>
+<TD>SequenceAlignment.java
+
+ This interface is designed to mimic a biological sequence alignment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractGappedSequence.html">AbstractGappedSequence</A></B></TD>
+<TD>AbstractGappedSequence.java
+
+
+ Created: Sat Mar 4 12:17:02 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequenceAlignment.html">AbstractSequenceAlignment</A></B></TD>
+<TD>AbstractSequenceAlignment.java
+
+ An abstract class to extend for the basic definition of a multiple
+ sequence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AlignmentColumn.html">AlignmentColumn</A></B></TD>
+<TD>AlignmentColumn.java
+
+ The Sequence and SequenceAlignment classes have been created to be fail-fast.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultGappedSequence.html">DefaultGappedSequence</A></B></TD>
+<TD>DefaultGappedSequence.java
+
+
+ Created: Sat Mar 4 12:28:57 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultSequenceAlignment.html">DefaultSequenceAlignment</A></B></TD>
+<TD>DefaultSequenceAlignment.java
+
+ A class to model the multiple sequence alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="EmptyGappedSequence.html">EmptyGappedSequence</A></B></TD>
+<TD>EmptyGappedSequence.java
+
+
+ Created: Tue Nov 7 18:15:06 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="EmptySequenceAlignment.html">EmptySequenceAlignment</A></B></TD>
+<TD>EmptySequenceAlignment.java
+
+
+ Created: Wed Apr 19 17:23:30 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Gap.html">Gap</A></B></TD>
+<TD>Gap.java
+
+
+ Created: Wed Mar 1 19:35:57 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SingleSequenceAlignment.html">SingleSequenceAlignment</A></B></TD>
+<TD>SingleSequenceAlignment.java
+
+ This class is for those stick occasions when you want a
+ SequenceAlignment but all you have is a Sequence.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoGapAtThisPositionException.html">NoGapAtThisPositionException</A></B></TD>
+<TD>NoGapAtThisPositionException.java
+
+
+ Created: Sat Mar 4 14:04:07 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoSuchSequenceException.html">NoSuchSequenceException</A></B></TD>
+<TD>NoSuchSequenceException.java
+
+ Alerts to an invalid sequence index within a sequence alignment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-tree.html
new file mode 100644
index 0000000..8d93deb
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/alignment/package-tree.html
@@ -0,0 +1,185 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.alignment Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.alignment Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.alignment
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>AbstractSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>AbstractMutableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html"><B>AbstractGappedSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.html"><B>DefaultGappedSequence</B></A></UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html"><B>AbstractSequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceList [...]
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.html"><B>DefaultSequenceAlignment</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.html"><B>SingleSequenceAlignment</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.html"><B>AlignmentColumn</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.html"><B>EmptyGappedSequence</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSeq [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html"><B>EmptySequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/Gap.html"><B>Gap</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>)
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.html"><B>NoGapAtThisPositionException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.html"><B>NoSuchSequenceException</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html"><B>AlignmentEventProvider</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>, uk.ac.man.bioi [...]
+</UL>
+<LI TYPE="circle">interface java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html"><B>EventListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>SequenceListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><B>VetoableSequenceListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiab [...]
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>Sequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A></UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEve [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>SequenceEventProvider</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html"><B>SequenceAlignment</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiab [...]
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html
new file mode 100644
index 0000000..58380ca
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html
@@ -0,0 +1,566 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+AbstractComplexSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractComplexSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class AbstractComplexSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/Sequenc [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html">DefaultComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractComplexSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></DL>
+
+<P>
+AbstractComplexSequence.java
+
+
+ Created: Fri Nov 24 13:33:32 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#AbstractComplexSequence(uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)">AbstractComplexSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement)">checkComplexSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement[])">checkComplexSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element)</CODE>
+
+<BR>
+ Check if all these elements are of a valid type</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexElementAtAsChar(int)">getComplexElementAtAsChar</A></B>(int index)</CODE>
+
+<BR>
+ Representing a ComplexElement as a char is not a simple task.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexSequenceAsChars()">getComplexSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexSequenceTypeException(uk.ac.man.bioinf.sequence.Element)">getComplexSequenceTypeException</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#getComplexType()">getComplexType</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">removeModificationAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected abstract <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)">setElementAtQuietly</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> element,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceIndexException(int)">getSequenceIndexExcept [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.ComplexSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/S [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractComplexSequence(uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)"><!-- --></A><H3>
+AbstractComplexSequence</H3>
+<PRE>
+public <B>AbstractComplexSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getComplexType()"><!-- --></A><H3>
+getComplexType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> <B>getComplexType</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkSequenceType(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+checkSequenceType</H3>
+<PRE>
+protected void <B>checkSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></CODE></B></DD>
+<DD>Check if all these elements are of a valid type
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element[])">checkSequenceType</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the elements
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE> - if an element is not of a
+ valid type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkSequenceType(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+checkSequenceType</H3>
+<PRE>
+protected void <B>checkSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkSequenceType(uk.ac.man.bioinf.sequence.Element)">checkSequenceType</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement[])"><!-- --></A><H3>
+checkComplexSequenceType</H3>
+<PRE>
+protected void <B>checkComplexSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] element)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><!-- --></A><H3>
+checkComplexSequenceType</H3>
+<PRE>
+protected void <B>checkComplexSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> element)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexSequenceTypeException(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+getComplexSequenceTypeException</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html">InvalidSequenceTypeException</A> <B>getComplexSequenceTypeException</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><!-- --></A><H3>
+addModificationAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>addModificationAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)"><!-- --></A><H3>
+setElementAtQuietly</H3>
+<PRE>
+protected abstract <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>setElementAtQuietly</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> element,
+ int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><!-- --></A><H3>
+removeModificationAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>removeModificationAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">removeModificationAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexElementAtAsChar(int)"><!-- --></A><H3>
+getComplexElementAtAsChar</H3>
+<PRE>
+public char[] <B>getComplexElementAtAsChar</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></CODE></B></DD>
+<DD>Representing a ComplexElement as a char is not a simple task. An
+ Element can have any number of Modifications each of which comes
+ with its own char representation. The following approach is
+ used. Each Element is represented first by its own char
+ representation, and then by its all of its modifications, and
+ then finally by an underscore _, which acts as a standard
+ terminator. Counting the number of underscores should show how
+ many Elements there are.
+ This is not meant to be a particular wonderfully parse-able
+ format.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAtAsChar(int)">getComplexElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD>a <code>char[]</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexSequenceAsChars()"><!-- --></A><H3>
+getComplexSequenceAsChars</H3>
+<PRE>
+public char[] <B>getComplexSequenceAsChars</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexSequenceAsChars()">getComplexSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html
new file mode 100644
index 0000000..ddb4e2b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html
@@ -0,0 +1,408 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:35 BST 2002 -->
+<TITLE>
+AbstractComplexSequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractComplexSequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractComplexSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class AbstractComplexSequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractSequenceType</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.AbstractComplexSequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractComplexSequenceType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></DL>
+
+<P>
+AbstractComplexSequenceType.java
+
+
+ Created: Tue Feb 29 22:10:30 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractComplexSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements">elements</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#AbstractComplexSequenceType(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification[], java.lang.String)">AbstractComplexSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] residues,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#AbstractComplexSequenceType(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification, java.lang.String)">AbstractComplexSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] residues,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#getModifications()">getModifications</A></B>()</CODE>
+
+<BR>
+ Gets all of the Modifications which are allowable in this
+ sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)">isAllowableElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem)</CODE>
+
+<BR>
+ Is this given element allowable in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)">isModification</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ Is this modification one which is allowable in this sequence
+ type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])">isModification</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</CODE>
+
+<BR>
+ Are these modifications allowable in this sequence type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()">getName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)">isElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])">isElement</A>, <A HREF="../../../.. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.SequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)">getElementForInt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getName()">getName</A>, <A HREF="../../../../. [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractComplexSequenceType(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification, java.lang.String)"><!-- --></A><H3>
+AbstractComplexSequenceType</H3>
+<PRE>
+public <B>AbstractComplexSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] residues,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AbstractComplexSequenceType(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification[], java.lang.String)"><!-- --></A><H3>
+AbstractComplexSequenceType</H3>
+<PRE>
+public <B>AbstractComplexSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] residues,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getModifications()"><!-- --></A><H3>
+getModifications</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] <B>getModifications</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Gets all of the Modifications which are allowable in this
+ sequence type. This should be immutable for a given instance of this.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#getModifications()">getModifications</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the modifications</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModification(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+isModification</H3>
+<PRE>
+public boolean <B>isModification</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Is this modification one which is allowable in this sequence
+ type. This should be immutable for a given instance of this.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)">isModification</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mod</CODE> - the modification
+<DT><B>Returns:</B><DD>true if the modification is allowable</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModification(uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+isModification</H3>
+<PRE>
+public boolean <B>isModification</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Are these modifications allowable in this sequence type. This
+ should be immutable.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])">isModification</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mod</CODE> - the modifications
+<DT><B>Returns:</B><DD>true if all the modifications are allowable</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><!-- --></A><H3>
+isAllowableElement</H3>
+<PRE>
+public boolean <B>isAllowableElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Is this given element allowable in this sequence type. A trivial
+ implementation of this would simply check if the ComplexElement
+ Residue is allowable, and all of the Modifications for this
+ ComplexElement are allowable. However there are other
+ possibilties if for instance not all Residues in a given sequence
+ type are Modifiable by all the allowable modifications
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)">isAllowableElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elem</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractComplexSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElement.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElement.html
new file mode 100644
index 0000000..8dcd99f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElement.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+ComplexElement
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexElement";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface ComplexElement</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html">DefaultComplexElement</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ComplexElement</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DL>
+
+<P>
+ComplexElement.java
+
+
+ Created: Mon Feb 28 20:41:07 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexElement.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html#getModifications()">getModifications</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html#getResidue()">getResidue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html#isModified(uk.ac.man.bioinf.sequence.complex.Modification)">isModified</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getResidue()"><!-- --></A><H3>
+getResidue</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> <B>getResidue</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModified(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+isModified</H3>
+<PRE>
+public boolean <B>isModified</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModifications()"><!-- --></A><H3>
+getModifications</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] <B>getModifications</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html
new file mode 100644
index 0000000..6f12c12
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html
@@ -0,0 +1,376 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:35 BST 2002 -->
+<TITLE>
+ComplexElementFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexElementFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElementFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class ComplexElementFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.ComplexElementFactory</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ComplexElementFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ComplexElementFactory.java
+
+
+ Created: Tue Feb 29 00:21:47 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexElementFactory.java,v 1.6 2001/08/16 14:30:21 white Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#ComplexElementFactory()">ComplexElementFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement[], uk.ac.man.bioinf.sequence.complex.Modification[])">addComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)">addComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification[])">addComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#addComplexElement(uk.ac.man.bioinf.sequence.Residue, uk.ac.man.bioinf.sequence.complex.Modification)">addComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#getComplexElement(uk.ac.man.bioinf.sequence.Residue)">getComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#removeComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)">removeComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html#setComplexElementFactory(uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface)">setComplexElementFactory</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A> factory)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ComplexElementFactory()"><!-- --></A><H3>
+ComplexElementFactory</H3>
+<PRE>
+public <B>ComplexElementFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="setComplexElementFactory(uk.ac.man.bioinf.sequence.complex.ComplexElementFactoryInterface)"><!-- --></A><H3>
+setComplexElementFactory</H3>
+<PRE>
+public static void <B>setComplexElementFactory</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html">ComplexElementFactoryInterface</A> factory)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexElement(uk.ac.man.bioinf.sequence.Residue)"><!-- --></A><H3>
+getComplexElement</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>getComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addComplexElement(uk.ac.man.bioinf.sequence.Residue, uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+addComplexElement</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>addComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+addComplexElement</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>addComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addComplexElement(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+addComplexElement</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] <B>addComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement[], uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+addComplexElement</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] <B>addComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+removeComplexElement</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>removeComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElementFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html
new file mode 100644
index 0000000..09a7769
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+ComplexElementFactoryInterface
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexElementFactoryInterface";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElementFactoryInterface.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface ComplexElementFactoryInterface</H2>
+<HR>
+<DL>
+<DT>public interface <B>ComplexElementFactoryInterface</B></DL>
+
+<P>
+ComplexElementFactoryInterface.java
+
+
+ Created: Wed Mar 1 12:40:54 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexElementFactoryInterface.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)">addComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#addComplexElement(uk.ac.man.bioinf.sequence.Residue, uk.ac.man.bioinf.sequence.complex.Modification)">addComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#getComplexElement(uk.ac.man.bioinf.sequence.Residue)">getComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> res)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html#removeComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)">removeComplexElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getComplexElement(uk.ac.man.bioinf.sequence.Residue)"><!-- --></A><H3>
+getComplexElement</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>getComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> res)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addComplexElement(uk.ac.man.bioinf.sequence.Residue, uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+addComplexElement</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>addComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> res,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+addComplexElement</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>addComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeComplexElement(uk.ac.man.bioinf.sequence.complex.ComplexElement, uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+removeComplexElement</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>removeComplexElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElementFactoryInterface.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexSequence.html
new file mode 100644
index 0000000..66401d3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexSequence.html
@@ -0,0 +1,355 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+ComplexSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface ComplexSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ComplexSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></DL>
+
+<P>
+ComplexSequence.java
+
+
+ Created: Wed Nov 22 17:56:08 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAtAsChar(int)">getComplexElementAtAsChar</A></B>(int index)</CODE>
+
+<BR>
+ Representing a ComplexElement as a char is not a simple task.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexSequenceAsChars()">getComplexSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">removeModificationAt</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/S [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><!-- --></A><H3>
+addModificationAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>addModificationAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)"><!-- --></A><H3>
+removeModificationAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>removeModificationAt</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod,
+ int index)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A>,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html">NoSuchModificationException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html">NoSuchModificationException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexElementAt(int)"><!-- --></A><H3>
+getComplexElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>getComplexElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexElementAtAsChar(int)"><!-- --></A><H3>
+getComplexElementAtAsChar</H3>
+<PRE>
+public char[] <B>getComplexElementAtAsChar</B>(int index)</PRE>
+<DL>
+<DD>Representing a ComplexElement as a char is not a simple task. An
+ Element can have any number of Modifications each of which comes
+ with its own char representation. The following approach is
+ used. Each Element is represented first by its own char
+ representation, and then by its all of its modifications, and
+ then finally by an underscore _, which acts as a standard
+ terminator. Counting the number of underscores should show how
+ many Elements there are.
+ This is not meant to be a particular wonderfully parse-able
+ format.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> -
+<DT><B>Returns:</B><DD>a <code>char[]</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexSequenceAsChars()"><!-- --></A><H3>
+getComplexSequenceAsChars</H3>
+<PRE>
+public char[] <B>getComplexSequenceAsChars</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html
new file mode 100644
index 0000000..b39fc14
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html
@@ -0,0 +1,317 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+ComplexSequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexSequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface ComplexSequenceType</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html">DefaultComplexSequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ComplexSequenceType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DL>
+
+<P>
+ComplexSequenceType.java
+
+
+ Created: Tue Feb 29 11:25:27 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#getModifications()">getModifications</A></B>()</CODE>
+
+<BR>
+ Gets all of the Modifications which are allowable in this
+ sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)">isAllowableElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem)</CODE>
+
+<BR>
+ Is this given element allowable in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)">isModification</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ Is this modification one which is allowable in this sequence
+ type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])">isModification</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</CODE>
+
+<BR>
+ Are these modifications allowable in this sequence type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.SequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)">getElementForInt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getName()">getName</A>, <A HREF="../../../../. [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getModifications()"><!-- --></A><H3>
+getModifications</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] <B>getModifications</B>()</PRE>
+<DL>
+<DD>Gets all of the Modifications which are allowable in this
+ sequence type. This should be immutable for a given instance of this.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the modifications</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModification(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+isModification</H3>
+<PRE>
+public boolean <B>isModification</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD>Is this modification one which is allowable in this sequence
+ type. This should be immutable for a given instance of this.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mod</CODE> - the modification
+<DT><B>Returns:</B><DD>true if the modification is allowable</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModification(uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+isModification</H3>
+<PRE>
+public boolean <B>isModification</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mod)</PRE>
+<DL>
+<DD>Are these modifications allowable in this sequence type. This
+ should be immutable.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mod</CODE> - the modifications
+<DT><B>Returns:</B><DD>true if all the modifications are allowable</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><!-- --></A><H3>
+isAllowableElement</H3>
+<PRE>
+public boolean <B>isAllowableElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem)</PRE>
+<DL>
+<DD>Is this given element allowable in this sequence type. A trivial
+ implementation of this would simply check if the ComplexElement
+ Residue is allowable, and all of the Modifications for this
+ ComplexElement are allowable. However there are other
+ possibilties if for instance not all Residues in a given sequence
+ type are Modifiable by all the allowable modifications
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elem</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html
new file mode 100644
index 0000000..12c33aa
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html
@@ -0,0 +1,346 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:35 BST 2002 -->
+<TITLE>
+DefaultComplexElement
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultComplexElement";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultComplexElement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class DefaultComplexElement</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.DefaultComplexElement</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultComplexElement</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></DL>
+
+<P>
+DefaultComplexElement.java
+
+
+ Created: Mon Feb 28 20:42:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultComplexElement.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#getModifications()">getModifications</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#getResidue()">getResidue</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#hashCode()">hashCode</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#isModified(uk.ac.man.bioinf.sequence.complex.Modification)">isModified</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html#toChar()">toChar</A></B>()</CODE>
+
+<BR>
+ Returns a character representation of this element.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#notify()">notify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#not [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toChar()"><!-- --></A><H3>
+toChar</H3>
+<PRE>
+public char <B>toChar</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></B></DD>
+<DD>Returns a character representation of this element. This may be
+ non-alphanumeric, and should be unique within a SequenceType.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the char representation<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><CODE>SequenceType</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getResidue()"><!-- --></A><H3>
+getResidue</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A> <B>getResidue</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html#getResidue()">getResidue</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModifications()"><!-- --></A><H3>
+getModifications</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] <B>getModifications</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html#getModifications()">getModifications</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModified(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+isModified</H3>
+<PRE>
+public boolean <B>isModified</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html#isModified(uk.ac.man.bioinf.sequence.complex.Modification)">isModified</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
+equals</H3>
+<PRE>
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="hashCode()"><!-- --></A><H3>
+hashCode</H3>
+<PRE>
+public int <B>hashCode</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultComplexElement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html
new file mode 100644
index 0000000..1a938d8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html
@@ -0,0 +1,450 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:35 BST 2002 -->
+<TITLE>
+DefaultComplexSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultComplexSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class DefaultComplexSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/Sequenc [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultComplexSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A></DL>
+
+<P>
+DefaultComplexSequence.java
+
+
+ Created: Fri Nov 24 14:08:23 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultComplexSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#DefaultComplexSequence(uk.ac.man.bioinf.sequence.complex.ComplexElement[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultComplexSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> identifier)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#DefaultComplexSequence(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">DefaultComplexSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> identifier)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getSequenceAsComplexElements()">getSequenceAsComplexElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)">setElementAtQuietly</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement)">checkComplexSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComple [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceIndexException(int)">getSequenceIndexExcept [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultComplexSequence(uk.ac.man.bioinf.sequence.Residue[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultComplexSequence</H3>
+<PRE>
+public <B>DefaultComplexSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> identifier)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="DefaultComplexSequence(uk.ac.man.bioinf.sequence.complex.ComplexElement[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+DefaultComplexSequence</H3>
+<PRE>
+public <B>DefaultComplexSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> identifier)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getComplexElementAt(int)"><!-- --></A><H3>
+getComplexElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>getComplexElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsComplexElements()"><!-- --></A><H3>
+getSequenceAsComplexElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] <B>getSequenceAsComplexElements</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)"><!-- --></A><H3>
+setElementAtQuietly</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>setElementAtQuietly</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)">setElementAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html
new file mode 100644
index 0000000..a2ace06
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html
@@ -0,0 +1,604 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:36 BST 2002 -->
+<TITLE>
+DefaultComplexSequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultComplexSequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultComplexSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class DefaultComplexSequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultComplexSequenceType</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></DL>
+
+<P>
+DefaultComplexSequenceType.java
+
+
+ Created: Mon Nov 27 16:05:27 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultComplexSequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#DefaultComplexSequenceType(uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.complex.Modification[], java.lang.String)">DefaultComplexSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mods,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getElementForInt(int)">getElementForInt</A></B>(int param1)</CODE>
+
+<BR>
+ The inverse of the method getIntForElement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getElements()">getElements</A></B>()</CODE>
+
+<BR>
+ Returns all the elements available in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> param1)</CODE>
+
+<BR>
+ This method is present as a performance enhancement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getModifications()">getModifications</A></B>()</CODE>
+
+<BR>
+ Gets all of the Modifications which are allowable in this
+ sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the human readable form of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)">isAllowableElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> element)</CODE>
+
+<BR>
+ Is this given element allowable in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(char)">isElement</A></B>(char param1)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(char[])">isElement</A></B>(char[] param1)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> param1)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] param1)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)">isModification</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</CODE>
+
+<BR>
+ Is this modification one which is allowable in this sequence
+ type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])">isModification</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mods)</CODE>
+
+<BR>
+ Are these modifications allowable in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html#size()">size</A></B>()</CODE>
+
+<BR>
+ Returns the number of elements in this sequence type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultComplexSequenceType(uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.complex.Modification[], java.lang.String)"><!-- --></A><H3>
+DefaultComplexSequenceType</H3>
+<PRE>
+public <B>DefaultComplexSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> type,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mods,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns the human readable form of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModifications()"><!-- --></A><H3>
+getModifications</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] <B>getModifications</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Gets all of the Modifications which are allowable in this
+ sequence type. This should be immutable for a given instance of this.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#getModifications()">getModifications</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the modifications</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModification(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+isModification</H3>
+<PRE>
+public boolean <B>isModification</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> mod)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Is this modification one which is allowable in this sequence
+ type. This should be immutable for a given instance of this.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification)">isModification</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mod</CODE> - the modification
+<DT><B>Returns:</B><DD>true if the modification is allowable</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isModification(uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+isModification</H3>
+<PRE>
+public boolean <B>isModification</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] mods)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Are these modifications allowable in this sequence type. This
+ should be immutable.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isModification(uk.ac.man.bioinf.sequence.complex.Modification[])">isModification</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>mods</CODE> - the modifications
+<DT><B>Returns:</B><DD>true if all the modifications are allowable</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)"><!-- --></A><H3>
+isAllowableElement</H3>
+<PRE>
+public boolean <B>isAllowableElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></B></DD>
+<DD>Is this given element allowable in this sequence type. A trivial
+ implementation of this would simply check if the ComplexElement
+ Residue is allowable, and all of the Modifications for this
+ ComplexElement are allowable. However there are other
+ possibilties if for instance not all Residues in a given sequence
+ type are Modifiable by all the allowable modifications
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html#isAllowableElement(uk.ac.man.bioinf.sequence.complex.ComplexElement)">isAllowableElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char[] param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char[])">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char)">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElements()"><!-- --></A><H3>
+getElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns all the elements available in this sequence type.
+ This array should be freely modifiable, and changes should not
+ percolate backwards iunto the internal data of the sequence
+ type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElements()">getElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementForInt(int)"><!-- --></A><H3>
+getElementForInt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementForInt</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>The inverse of the method getIntForElement.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)">getElementForInt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - a value of type 'int'
+<DT><B>Returns:</B><DD>a value of type 'Element'</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIntForElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+getIntForElement</H3>
+<PRE>
+public int <B>getIntForElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>This method is present as a performance enhancement. For every
+ Element this method should return a unique and repeatable int,
+ starting at 0 and ending at size() - 1 for all possible
+ Elements. This enables the Element to be used as an index for an
+ array which in turn allows implementation of efficient look up
+ tables, rather than using a hashtable.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the element
+<DT><B>Returns:</B><DD>a int</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns the number of elements in this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#size()">size</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of elements</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultComplexSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html
new file mode 100644
index 0000000..262a5fa
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html
@@ -0,0 +1,910 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:36 BST 2002 -->
+<TITLE>
+DefaultGappedComplexSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultGappedComplexSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultGappedComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class DefaultGappedComplexSequence</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">uk.ac.man.bioinf.sequence.AbstractSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">uk.ac.man.bioinf.sequence.AbstractMutableSequence</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.DefaultGappedComplexSequence</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../ [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultGappedComplexSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A></DL>
+
+<P>
+DefaultGappedComplexSequence.java
+
+
+ Created: Tue Dec 5 16:55:11 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultGappedComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#DefaultGappedComplexSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)">DefaultGappedComplexSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#deleteGapAt(int)">deleteGapAt</A></B>(int param1)</CODE>
+
+<BR>
+ Delete the element at index.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#deleteGapAt(int, int)">deleteGapAt</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Delete the elements starting at index for the specified length</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementAt(int)">getElementAt</A></B>(int index)</CODE>
+
+<BR>
+ Returns an element at a given location.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></B>(int param1)</CODE>
+
+<BR>
+ Returns the character of an target element.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)">getElementsAsGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] param1,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> param2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)">getElementsAsGappedSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] param1,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> param2,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> param3)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedElementAt(int)">getGappedElementAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></B>(int param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedLength()">getGappedLength</A></B>()</CODE>
+
+<BR>
+ Returns the gapped length of this sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></B>(int param1)</CODE>
+
+<BR>
+ Translate between the gapped index, and the ungapped index</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSequenceAsChars()">getSequenceAsChars</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of characters.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSequenceAsComplexElements()">getSequenceAsComplexElements</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSequenceAsElements()">getSequenceAsElements</A></B>()</CODE>
+
+<BR>
+ Returns the sequence as an array of elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getSubSequence(int, int)">getSubSequence</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Returns a sub-sequence from the current sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></B>(int param1)</CODE>
+
+<BR>
+ Translate between the gapped position and the ungapped
+ position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#insertGapAt(int)">insertGapAt</A></B>(int param1)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#insertGapAt(int, int)">insertGapAt</A></B>(int param1,
+ int param2)</CODE>
+
+<BR>
+ Inserts the elements at this position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)">setElementAtQuietly</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.AbstractComplexSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComplexSequenceType(uk.ac.man.bioinf.sequence.complex.ComplexElement)">checkComplexSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#checkComple [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractMutableSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html#fireSequenceEvent(uk [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.AbstractSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html">AbstractSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#checkRange(int)">checkRange</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceIndexException(int)">getSequenceIndexException</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceType()">getSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceTypeException(uk.ac.man.bioinf.sequ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceType()">getSequenceType</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.ComplexSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAtAsChar(int)">getComplexElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexSequenceAsChars()">getComplexSequenceAsChars</A>, <A HREF="../../../ [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultGappedComplexSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.complex.ComplexSequenceType)"><!-- --></A><H3>
+DefaultGappedComplexSequence</H3>
+<PRE>
+public <B>DefaultGappedComplexSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getComplexElementAt(int)"><!-- --></A><H3>
+getComplexElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>getComplexElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAt(int)"><!-- --></A><H3>
+getElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns an element at a given location.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAt(int)"><!-- --></A><H3>
+getGappedElementAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getGappedElementAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsComplexElements()"><!-- --></A><H3>
+getSequenceAsComplexElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A>[] <B>getSequenceAsComplexElements</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)"><!-- --></A><H3>
+setElementAtQuietly</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> <B>setElementAtQuietly</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">ComplexElement</A> elem,
+ int index)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html#setElementAtQuietly(uk.ac.man.bioinf.sequence.complex.ComplexElement, int)">setElementAtQuietly</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType, uk.ac.man.bioinf.sequence.identifier.Identifier)"><!-- --></A><H3>
+getElementsAsGappedSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getElementsAsGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] param1,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> param2,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> param3)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementsAsGappedSequence(uk.ac.man.bioinf.sequence.Element[], uk.ac.man.bioinf.sequence.SequenceType)"><!-- --></A><H3>
+getElementsAsGappedSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getElementsAsGappedSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] param1,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> param2)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsElements()"><!-- --></A><H3>
+getSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getSequenceAsElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of elements.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsElements()">getSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the length of the sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length of the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSubSequence(int, int)"><!-- --></A><H3>
+getGappedSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getGappedSubSequence</B>(int param1,
+ int param2)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSubSequence(int, int)">getGappedSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsElements()"><!-- --></A><H3>
+getGappedSequenceAsElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getGappedSequenceAsElements</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsElements()">getGappedSequenceAsElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedLength()"><!-- --></A><H3>
+getGappedLength</H3>
+<PRE>
+public int <B>getGappedLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Returns the gapped length of this sequence. That is the length of
+ the sequence including its gaps. Conversely this means that the
+ getLength method of the Sequence interface returns the length of
+ the sequence ignoring the gaps.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedLength()">getGappedLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the length</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedPositionOf(int)"><!-- --></A><H3>
+getGappedPositionOf</H3>
+<PRE>
+public int <B>getGappedPositionOf</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped index, and the ungapped index
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedPositionOf(int)">getGappedPositionOf</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the ungapped position
+<DT><B>Returns:</B><DD>the gapped position of the equivalent element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getUngappedPositionOf(int)"><!-- --></A><H3>
+getUngappedPositionOf</H3>
+<PRE>
+public int <B>getUngappedPositionOf</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Translate between the gapped position and the ungapped
+ position. I havent quite decided what to do at the moment if the
+ index refers to a gap. One idea is to throw a
+ NoSuchSequenceElementException which makes a certain amount of
+ sense but isnt really that useful. Perhaps a better idea is to
+ run -(insertion-point) where the insertion point is the nearest
+ element before the current requested position which is not a
+ gap. That way a value less than 0 would indicate a gap and would
+ also return a useful value
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getUngappedPositionOf(int)">getUngappedPositionOf</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> -
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int param1)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int)">insertGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="insertGapAt(int, int)"><!-- --></A><H3>
+insertGapAt</H3>
+<PRE>
+public void <B>insertGapAt</B>(int param1,
+ int param2)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Inserts the elements at this position. If the index is one longer
+ than the length of the sequence the sequence will be extended.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#insertGapAt(int, int)">insertGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the index at which to insert
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int param1)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Delete the element at index.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the index to delete
+<DT><B>Returns:</B><DD>the element which has just been deleted
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="deleteGapAt(int, int)"><!-- --></A><H3>
+deleteGapAt</H3>
+<PRE>
+public void <B>deleteGapAt</B>(int param1,
+ int param2)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></B></DD>
+<DD>Delete the elements starting at index for the specified length
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the index to start at<DD><CODE>param2</CODE> - the length to delete
+<DT><B>Returns:</B><DD>the elements just deleted
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedElementAtAsChar(int)"><!-- --></A><H3>
+getGappedElementAtAsChar</H3>
+<PRE>
+public char <B>getGappedElementAtAsChar</B>(int param1)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(int)">getGappedElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAsChars()"><!-- --></A><H3>
+getGappedSequenceAsChars</H3>
+<PRE>
+public char[] <B>getGappedSequenceAsChars</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedSequenceAsChars()">getGappedSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubSequence(int, int)"><!-- --></A><H3>
+getSubSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getSubSequence</B>(int param1,
+ int param2)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns a sub-sequence from the current sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSubSequence(int, int)">getSubSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSubSequence(int, int)">getSubSequence</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Abstrac [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the initial index of the sub-sequence
+<DT><B>Returns:</B><DD>the sub-sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAsChars()"><!-- --></A><H3>
+getSequenceAsChars</H3>
+<PRE>
+public char[] <B>getSequenceAsChars</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the sequence as an array of characters.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getSequenceAsChars()">getSequenceAsChars</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Abstrac [...]
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementAtAsChar(int)"><!-- --></A><H3>
+getElementAtAsChar</H3>
+<PRE>
+public char <B>getElementAtAsChar</B>(int param1)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></B></DD>
+<DD>Returns the character of an target element.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE><DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html#getElementAtAsChar(int)">getElementAtAsChar</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/A [...]
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>param1</CODE> - the location of the target element
+<DT><B>Returns:</B><DD>the element character</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultGappedComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html
new file mode 100644
index 0000000..b33232f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html
@@ -0,0 +1,231 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+GappedComplexSequence
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappedComplexSequence";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface GappedComplexSequence</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequenc [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>GappedComplexSequence</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></DL>
+
+<P>
+GappedComplexSequence.java
+
+ Place holder type interface.
+
+ Created: Tue Dec 5 16:55:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappedComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.alignment.GappedSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#deleteGapAt(int, int)">deleteGapAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAt(int)">getGappedElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html#getGappedElementAtAsChar(i [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Sequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAt(int)">getElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getElementAtAsChar(int)">getElementAtAsChar</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html#getSequenceAsChars()">getSequenceAsChars</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/S [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifiable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEventProvider"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSe [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.ComplexSequence"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#addModificationAt(uk.ac.man.bioinf.sequence.complex.Modification, int)">addModificationAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAt(int)">getComplexElementAt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html#getComplexElementAtAsChar(int)">getComplexElementAtAsChar</A>, <A HREF="../../../../../../ [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedComplexSequence.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html
new file mode 100644
index 0000000..dd237db
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html
@@ -0,0 +1,326 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+HardModificationSetFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="HardModificationSetFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="HardModificationSetFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class HardModificationSetFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.HardModificationSetFactory</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>HardModificationSetFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></DL>
+
+<P>
+HardModificationSetFactory.java
+
+
+ Created: Wed Mar 1 15:04:37 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: HardModificationSetFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#HardModificationSetFactory()">HardModificationSetFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet()">getModificationSet</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="HardModificationSetFactory()"><!-- --></A><H3>
+HardModificationSetFactory</H3>
+<PRE>
+public <B>HardModificationSetFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getModificationSet()"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet()">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="HardModificationSetFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html
new file mode 100644
index 0000000..bd92fe2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+IllegalDuplicateModificationException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="IllegalDuplicateModificationException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IllegalDuplicateModificationException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class IllegalDuplicateModificationException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>IllegalDuplicateModificationException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+IllegalDuplicateModificationException.java
+
+
+ Created: Mon Feb 28 23:57:13 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: IllegalDuplicateModificationException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.complex.IllegalDuplicateModificationException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html#IllegalDuplicateModificationException(java.lang.String)">IllegalDuplicateModificationException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IllegalDuplicateModificationException(java.lang.String)"><!-- --></A><H3>
+IllegalDuplicateModificationException</H3>
+<PRE>
+public <B>IllegalDuplicateModificationException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IllegalDuplicateModificationException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/Methylation.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/Methylation.html
new file mode 100644
index 0000000..1251170
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/Methylation.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+Methylation
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Methylation";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Methylation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.SingletonModification">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class Methylation</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--uk.ac.man.bioinf.sequence.complex.AbstractModification
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html">uk.ac.man.bioinf.sequence.complex.SingletonModification</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.Methylation</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>Methylation</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html">SingletonModification</A></DL>
+
+<P>
+Methylation.java
+
+
+ Created: Tue Feb 29 11:44:59 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Methylation.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html">Methylation</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html#METHYLATION">METHYLATION</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.SingletonModification"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html">SingletonModification</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html#getName()">getName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="METHYLATION"><!-- --></A><H3>
+METHYLATION</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html">Methylation</A> <B>METHYLATION</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Methylation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.complex.SingletonModification">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/Modification.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/Modification.html
new file mode 100644
index 0000000..53bb404
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/Modification.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+Modification
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Modification";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Modification.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface Modification</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD>uk.ac.man.bioinf.sequence.complex.AbstractModification</DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Modification</B></DL>
+
+<P>
+Modification.java
+
+
+ Created: Mon Feb 28 20:42:16 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Modification.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html#toChar()">toChar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toChar()"><!-- --></A><H3>
+toChar</H3>
+<PRE>
+public char <B>toChar</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Modification.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ModificationFactory.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ModificationFactory.html
new file mode 100644
index 0000000..4403b91
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ModificationFactory.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+ModificationFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModificationFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModificationFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class ModificationFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.ModificationFactory</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ModificationFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ModificationFactory.java
+
+
+ Created: Mon Feb 28 23:07:50 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModificationFactory.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html#ModificationFactory()">ModificationFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html#createModification(java.lang.String, char)">createModification</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ char toChar)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html#getModification(java.lang.String)">getModification</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ModificationFactory()"><!-- --></A><H3>
+ModificationFactory</H3>
+<PRE>
+public <B>ModificationFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getModification(java.lang.String)"><!-- --></A><H3>
+getModification</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> <B>getModification</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createModification(java.lang.String, char)"><!-- --></A><H3>
+createModification</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> <B>createModification</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name,
+ char toChar)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModificationFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html
new file mode 100644
index 0000000..7d3c192
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+ModificationSetFactoryInterface
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ModificationSetFactoryInterface";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModificationSetFactoryInterface.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Interface ModificationSetFactoryInterface</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html">HardModificationSetFactory</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html">WeakModificationSetFactory</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ModificationSetFactoryInterface</B></DL>
+
+<P>
+ModificationSetFactoryInterface.java
+
+
+ Created: Wed Mar 1 15:01:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ModificationSetFactoryInterface.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet()">getModificationSet</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getModificationSet()"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ModificationSetFactoryInterface.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html
new file mode 100644
index 0000000..82a4ec2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+NoSuchModificationException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoSuchModificationException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchModificationException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class NoSuchModificationException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.NoSuchModificationException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoSuchModificationException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">RuntimeException</A></DL>
+
+<P>
+NoSuchModificationException.java
+
+
+ Created: Tue Feb 29 00:09:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoSuchModificationException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.complex.NoSuchModificationException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html#NoSuchModificationException(java.lang.String)">NoSuchModificationException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoSuchModificationException(java.lang.String)"><!-- --></A><H3>
+NoSuchModificationException</H3>
+<PRE>
+public <B>NoSuchModificationException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSuchModificationException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/SingletonModification.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/SingletonModification.html
new file mode 100644
index 0000000..ba49e82
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/SingletonModification.html
@@ -0,0 +1,258 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+SingletonModification
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SingletonModification";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingletonModification.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class SingletonModification</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--uk.ac.man.bioinf.sequence.complex.AbstractModification
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.SingletonModification</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html">Methylation</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SingletonModification</B><DT>extends uk.ac.man.bioinf.sequence.complex.AbstractModification</DL>
+
+<P>
+SingletonModification.java
+
+
+ Created: Mon Feb 28 23:16:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SingletonModification.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html#toChar()">toChar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toChar()"><!-- --></A><H3>
+toChar</H3>
+<PRE>
+public char <B>toChar</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html#toChar()">toChar</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SingletonModification.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html
new file mode 100644
index 0000000..f3b8cef
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html
@@ -0,0 +1,326 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+WeakModificationSetFactory
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="WeakModificationSetFactory";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WeakModificationSetFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.complex</FONT>
+<BR>
+Class WeakModificationSetFactory</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.complex.WeakModificationSetFactory</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>WeakModificationSetFactory</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></DL>
+
+<P>
+WeakModificationSetFactory.java
+
+
+ Created: Wed Mar 1 15:09:49 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: WeakModificationSetFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#WeakModificationSetFactory()">WeakModificationSetFactory</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet()">getModificationSet</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> uk.ac.man.bioinf.sequence.complex.ModificationSet</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="WeakModificationSetFactory()"><!-- --></A><H3>
+WeakModificationSetFactory</H3>
+<PRE>
+public <B>WeakModificationSetFactory</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getModificationSet()"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet()">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[])">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)"><!-- --></A><H3>
+getModificationSet</H3>
+<PRE>
+public uk.ac.man.bioinf.sequence.complex.ModificationSet <B>getModificationSet</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>[] modifications,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A> modification)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html#getModificationSet(uk.ac.man.bioinf.sequence.complex.Modification[], uk.ac.man.bioinf.sequence.complex.Modification)">getModificationSet</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="WeakModificationSetFactory.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-frame.html
new file mode 100644
index 0000000..b81140e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-frame.html
@@ -0,0 +1,90 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.complex()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.complex()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.complex</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ComplexElement.html" TARGET="classFrame"><I>ComplexElement</I></A>
+<BR>
+<A HREF="ComplexElementFactoryInterface.html" TARGET="classFrame"><I>ComplexElementFactoryInterface</I></A>
+<BR>
+<A HREF="ComplexSequence.html" TARGET="classFrame"><I>ComplexSequence</I></A>
+<BR>
+<A HREF="ComplexSequenceType.html" TARGET="classFrame"><I>ComplexSequenceType</I></A>
+<BR>
+<A HREF="GappedComplexSequence.html" TARGET="classFrame"><I>GappedComplexSequence</I></A>
+<BR>
+<A HREF="Modification.html" TARGET="classFrame"><I>Modification</I></A>
+<BR>
+<A HREF="ModificationSetFactoryInterface.html" TARGET="classFrame"><I>ModificationSetFactoryInterface</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractComplexSequence.html" TARGET="classFrame">AbstractComplexSequence</A>
+<BR>
+<A HREF="AbstractComplexSequenceType.html" TARGET="classFrame">AbstractComplexSequenceType</A>
+<BR>
+<A HREF="ComplexElementFactory.html" TARGET="classFrame">ComplexElementFactory</A>
+<BR>
+<A HREF="DefaultComplexElement.html" TARGET="classFrame">DefaultComplexElement</A>
+<BR>
+<A HREF="DefaultComplexSequence.html" TARGET="classFrame">DefaultComplexSequence</A>
+<BR>
+<A HREF="DefaultComplexSequenceType.html" TARGET="classFrame">DefaultComplexSequenceType</A>
+<BR>
+<A HREF="DefaultGappedComplexSequence.html" TARGET="classFrame">DefaultGappedComplexSequence</A>
+<BR>
+<A HREF="HardModificationSetFactory.html" TARGET="classFrame">HardModificationSetFactory</A>
+<BR>
+<A HREF="Methylation.html" TARGET="classFrame">Methylation</A>
+<BR>
+<A HREF="ModificationFactory.html" TARGET="classFrame">ModificationFactory</A>
+<BR>
+<A HREF="SingletonModification.html" TARGET="classFrame">SingletonModification</A>
+<BR>
+<A HREF="WeakModificationSetFactory.html" TARGET="classFrame">WeakModificationSetFactory</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="IllegalDuplicateModificationException.html" TARGET="classFrame">IllegalDuplicateModificationException</A>
+<BR>
+<A HREF="NoSuchModificationException.html" TARGET="classFrame">NoSuchModificationException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-summary.html
new file mode 100644
index 0000000..e254b04
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-summary.html
@@ -0,0 +1,314 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.complex()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.complex()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.complex
+</H2>
+Provides complex sequence support.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexElement.html"><I>ComplexElement</I></A></B></TD>
+<TD>ComplexElement.java
+
+
+ Created: Mon Feb 28 20:41:07 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexElementFactoryInterface.html"><I>ComplexElementFactoryInterface</I></A></B></TD>
+<TD>ComplexElementFactoryInterface.java
+
+
+ Created: Wed Mar 1 12:40:54 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexSequence.html"><I>ComplexSequence</I></A></B></TD>
+<TD>ComplexSequence.java
+
+
+ Created: Wed Nov 22 17:56:08 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexSequenceType.html"><I>ComplexSequenceType</I></A></B></TD>
+<TD>ComplexSequenceType.java
+
+
+ Created: Tue Feb 29 11:25:27 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappedComplexSequence.html"><I>GappedComplexSequence</I></A></B></TD>
+<TD>GappedComplexSequence.java
+
+ Place holder type interface.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Modification.html"><I>Modification</I></A></B></TD>
+<TD>Modification.java
+
+
+ Created: Mon Feb 28 20:42:16 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModificationSetFactoryInterface.html"><I>ModificationSetFactoryInterface</I></A></B></TD>
+<TD>ModificationSetFactoryInterface.java
+
+
+ Created: Wed Mar 1 15:01:48 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractComplexSequence.html">AbstractComplexSequence</A></B></TD>
+<TD>AbstractComplexSequence.java
+
+
+ Created: Fri Nov 24 13:33:32 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractComplexSequenceType.html">AbstractComplexSequenceType</A></B></TD>
+<TD>AbstractComplexSequenceType.java
+
+
+ Created: Tue Feb 29 22:10:30 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexElementFactory.html">ComplexElementFactory</A></B></TD>
+<TD>ComplexElementFactory.java
+
+
+ Created: Tue Feb 29 00:21:47 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultComplexElement.html">DefaultComplexElement</A></B></TD>
+<TD>DefaultComplexElement.java
+
+
+ Created: Mon Feb 28 20:42:48 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultComplexSequence.html">DefaultComplexSequence</A></B></TD>
+<TD>DefaultComplexSequence.java
+
+
+ Created: Fri Nov 24 14:08:23 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultComplexSequenceType.html">DefaultComplexSequenceType</A></B></TD>
+<TD>DefaultComplexSequenceType.java
+
+
+ Created: Mon Nov 27 16:05:27 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultGappedComplexSequence.html">DefaultGappedComplexSequence</A></B></TD>
+<TD>DefaultGappedComplexSequence.java
+
+
+ Created: Tue Dec 5 16:55:11 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="HardModificationSetFactory.html">HardModificationSetFactory</A></B></TD>
+<TD>HardModificationSetFactory.java
+
+
+ Created: Wed Mar 1 15:04:37 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Methylation.html">Methylation</A></B></TD>
+<TD>Methylation.java
+
+
+ Created: Tue Feb 29 11:44:59 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ModificationFactory.html">ModificationFactory</A></B></TD>
+<TD>ModificationFactory.java
+
+
+ Created: Mon Feb 28 23:07:50 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SingletonModification.html">SingletonModification</A></B></TD>
+<TD>SingletonModification.java
+
+
+ Created: Mon Feb 28 23:16:04 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="WeakModificationSetFactory.html">WeakModificationSetFactory</A></B></TD>
+<TD>WeakModificationSetFactory.java
+
+
+ Created: Wed Mar 1 15:09:49 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="IllegalDuplicateModificationException.html">IllegalDuplicateModificationException</A></B></TD>
+<TD>IllegalDuplicateModificationException.java
+
+
+ Created: Mon Feb 28 23:57:13 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoSuchModificationException.html">NoSuchModificationException</A></B></TD>
+<TD>NoSuchModificationException.java
+
+
+ Created: Tue Feb 29 00:09:26 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package uk.ac.man.bioinf.sequence.complex Description
+</H2>
+
+<P>
+Provides complex sequence support. Complex sequences are those
+ sequences which are mostly one kind of sequence, but not quite! An
+ example would be a DNA sequence carrying information about
+ methylation status with it.
+<P>
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-tree.html
new file mode 100644
index 0000000..6b4e24d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/complex/package-tree.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.complex Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.complex Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.complex
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.AbstractModification (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html">Modification</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/SingletonModification.html"><B>SingletonModification</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Methylation.html"><B>Methylation</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>AbstractSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>AbstractMutableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html"><B>AbstractComplexSequence</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.html"><B>DefaultComplexSequence</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.html"><B>DefaultGappedComplexSequence</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComp [...]
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>AbstractSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html"><B>AbstractComplexSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>)
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.html"><B>ComplexElementFactory</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.html"><B>DefaultComplexElement</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html">Compl [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.html"><B>DefaultComplexSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html">ComplexSequenceType</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.html"><B>HardModificationSetFactory</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationFactory.html"><B>ModificationFactory</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.html"><B>IllegalDuplicateModificationException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.html"><B>NoSuchModificationException</B></A></UL>
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.html"><B>WeakModificationSetFactory</B></A> (implements uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html">ModificationSetFactoryInterface</A>)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.html"><B>ComplexElementFactoryInterface</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>Element</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexElement.html"><B>ComplexElement</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>Sequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>ComplexSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> (also extends uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>)
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>)
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/Modification.html"><B>Modification</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.html"><B>ModificationSetFactoryInterface</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/Seque [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html"><B>GappedComplexSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>)
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><B>SequenceType</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.html"><B>ComplexSequenceType</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEvent.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEvent.html
new file mode 100644
index 0000000..6d2fb31
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEvent.html
@@ -0,0 +1,387 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Class SequenceEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.event.SequenceEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceEvent</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></DL>
+
+<P>
+SequenceEvent.java
+
+ Instances of this class represent an event to a sequence. It
+ includes reference to the location of the event, as well as
+ its type.
+
+ Created: Tue Feb 15 19:12:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceEvent.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.event.SequenceEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#SequenceEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)">SequenceEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int length,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</CODE>
+
+<BR>
+ Constructor to set the event source, location and type, which allows
+ the definition of the start and end of an event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#SequenceEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)">SequenceEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</CODE>
+
+<BR>
+ Constructor to set the event source, location and type.</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the end location of the event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getStart()">getStart</A></B>()</CODE>
+
+<BR>
+ Returns the start location of the event.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getType()">getType</A></B>()</CODE>
+
+<BR>
+ Returns the seqyence event type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><!-- --></A><H3>
+SequenceEvent</H3>
+<PRE>
+public <B>SequenceEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</PRE>
+<DL>
+<DD>Constructor to set the event source, location and type.
+<P>
+<DT><B>Parameters:</B><DD><CODE>src</CODE> - the source of the event (i.e: the sequence)<DD><CODE>location</CODE> - the location of the event<DD><CODE>type</CODE> - the sequence event type</DL>
+<HR>
+
+<A NAME="SequenceEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><!-- --></A><H3>
+SequenceEvent</H3>
+<PRE>
+public <B>SequenceEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int length,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</PRE>
+<DL>
+<DD>Constructor to set the event source, location and type, which allows
+ the definition of the start and end of an event.
+<P>
+<DT><B>Parameters:</B><DD><CODE>src</CODE> - the source of the event (i.e: the sequence)<DD><CODE>start</CODE> - the start location of the event<DD><CODE>type</CODE> - the sequence event type</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getStart()"><!-- --></A><H3>
+getStart</H3>
+<PRE>
+public int <B>getStart</B>()</PRE>
+<DL>
+<DD>Returns the start location of the event.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the start</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD>Returns the end location of the event.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the end</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getType()"><!-- --></A><H3>
+getType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>getType</B>()</PRE>
+<DL>
+<DD>Returns the seqyence event type.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html
new file mode 100644
index 0000000..f2aab2e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html
@@ -0,0 +1,284 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+SequenceEventProvider
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceEventProvider";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceEventProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Interface SequenceEventProvider</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.html">GappedComplexSequence</A>, <A H [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">AbstractMutableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">Abst [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceEventProvider</B></DL>
+
+<P>
+SequenceEventProvider.java
+
+ An interface designed to enforce the methods necessary to listen to a
+ sequence.
+
+ Created: Thu Mar 2 18:22:26 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceEventProvider.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified vetoable sequence listener.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD>Adds the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD>Removes the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD>Adds the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD>Removes the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceEventProvider.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEventType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEventType.html
new file mode 100644
index 0000000..340d963
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceEventType.html
@@ -0,0 +1,354 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceEventType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceEventType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceEventType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Class SequenceEventType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.event.SequenceEventType</B>
+</PRE>
+<HR>
+<DL>
+<DT>public final class <B>SequenceEventType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></DL>
+
+<P>
+SequenceEventType.java
+
+ This class provides an enumerated type for the SequenceEvent class
+ to pass around as an identifier
+
+ Created: Tue Feb 15 20:10:48 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceEventType.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html#DELETE">DELETE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html#GAPDELETE">GAPDELETE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html#GAPINSERT">GAPINSERT</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html#INSERT">INSERT</A></B></CODE>
+
+<BR>
+ Indicates a insertion event</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html#SET">SET</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html#UNSPECIFIED">UNSPECIFIED</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="INSERT"><!-- --></A><H3>
+INSERT</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>INSERT</B></PRE>
+<DL>
+<DD>Indicates a insertion event
+<P>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="DELETE"><!-- --></A><H3>
+DELETE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>DELETE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="SET"><!-- --></A><H3>
+SET</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>SET</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GAPINSERT"><!-- --></A><H3>
+GAPINSERT</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>GAPINSERT</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GAPDELETE"><!-- --></A><H3>
+GAPDELETE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>GAPDELETE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="UNSPECIFIED"><!-- --></A><H3>
+UNSPECIFIED</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> <B>UNSPECIFIED</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceEventType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceListener.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceListener.html
new file mode 100644
index 0000000..1d2e6d5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceListener.html
@@ -0,0 +1,224 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Interface SequenceListener</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.html">ConsensusPercentageIDColorMap</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.html">DefaultConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceListener</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A></DL>
+
+<P>
+SequenceListener.java
+
+ Listens for events occuring to a sequence
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceListener.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><CODE>Created: Tue Feb 15 18:24:38 2000</CODE></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html
new file mode 100644
index 0000000..ed2987e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html
@@ -0,0 +1,391 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceListenerSupport
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceListenerSupport";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Class SequenceListenerSupport</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.event.SequenceListenerSupport</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceListenerSupport</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceListenerSupport.java
+
+ This class provides support and handles the listeners to a specific
+ sequence. This ofcourse means there is one support object for one
+ sequence object.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceListenerSupport.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><CODE>Created: Wed Feb 16 19:28:44 2000</CODE></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#SequenceListenerSupport()">SequenceListenerSupport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds a sequence listener object to a Vector of listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds a vetoable sequence listener to the Vector of listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#fireSequenceEvent(uk.ac.man.bioinf.sequence.event.SequenceEvent)">fireSequenceEvent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ This function fires the sequence event to all the interested listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#fireVetoableSequenceEvent(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">fireVetoableSequenceEvent</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ This function fires the vetoable event to the vetoable listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#hasListeners()">hasListeners</A></B>()</CODE>
+
+<BR>
+ There is really no point in making an event object if there are
+ no listeners.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes a sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable sequence listener.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceListenerSupport()"><!-- --></A><H3>
+SequenceListenerSupport</H3>
+<PRE>
+public <B>SequenceListenerSupport</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="hasListeners()"><!-- --></A><H3>
+hasListeners</H3>
+<PRE>
+public boolean <B>hasListeners</B>()</PRE>
+<DL>
+<DD>There is really no point in making an event object if there are
+ no listeners. This method allows other classes to be intelligent
+ about the way it does things.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>a <code>boolean</code> value</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireSequenceEvent(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+fireSequenceEvent</H3>
+<PRE>
+public void <B>fireSequenceEvent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD>This function fires the sequence event to all the interested listeners.
+ It also fires to the vetoable listeners, which are stored separately,
+ because the interface for VetoableSequenceListener extends the
+ SequenceListener interface.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event to be fired<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><CODE>VetoableSequenceListener</CODE></A>,
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><CODE>SequenceListener</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireVetoableSequenceEvent(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+fireVetoableSequenceEvent</H3>
+<PRE>
+public void <B>fireVetoableSequenceEvent</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>This function fires the vetoable event to the vetoable listeners.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event to be fired
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD>Adds a sequence listener object to a Vector of listeners.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD>Removes a sequence listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD>Adds a vetoable sequence listener to the Vector of listeners.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD>Removes a vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceVetoException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceVetoException.html
new file mode 100644
index 0000000..7aae82b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/SequenceVetoException.html
@@ -0,0 +1,276 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceVetoException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceVetoException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceVetoException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Class SequenceVetoException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.event.SequenceVetoException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceVetoException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">Exception</A></DL>
+
+<P>
+SequenceVetoException.java
+
+ An exception thrown when an object vetos a sequence change event.
+
+ Created: Tue Feb 15 21:08:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceVetoException.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.event.SequenceVetoException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html#SequenceVetoException(java.lang.String, uk.ac.man.bioinf.sequence.event.SequenceEvent)">SequenceVetoException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ The constructor; storing the event as well as source</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html#getEvent()">getEvent</A></B>()</CODE>
+
+<BR>
+ Returns the sequence event that the veto objected to</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceVetoException(java.lang.String, uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+SequenceVetoException</H3>
+<PRE>
+public <B>SequenceVetoException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD>The constructor; storing the event as well as source
+<P>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getEvent()"><!-- --></A><H3>
+getEvent</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> <B>getEvent</B>()</PRE>
+<DL>
+<DD>Returns the sequence event that the veto objected to
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence event</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceVetoException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html
new file mode 100644
index 0000000..eb7d130
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html
@@ -0,0 +1,285 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+VetoableSequenceEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VetoableSequenceEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableSequenceEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEvent">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Class VetoableSequenceEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">uk.ac.man.bioinf.sequence.event.SequenceEvent</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>VetoableSequenceEvent</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A></DL>
+
+<P>
+VetoableSequenceEvent.java
+
+
+ Created: Fri Feb 18 17:38:50 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VetoableSequenceEvent.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html#VetoableSequenceEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)">VetoableSequenceEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int length,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html#VetoableSequenceEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)">VetoableSequenceEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEvent"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getLength()">getLength</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getStart()">getStart</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#getType()">getType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="VetoableSequenceEvent(java.lang.Object, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><!-- --></A><H3>
+VetoableSequenceEvent</H3>
+<PRE>
+public <B>VetoableSequenceEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int location,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="VetoableSequenceEvent(java.lang.Object, int, int, uk.ac.man.bioinf.sequence.event.SequenceEventType)"><!-- --></A><H3>
+VetoableSequenceEvent</H3>
+<PRE>
+public <B>VetoableSequenceEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> src,
+ int start,
+ int length,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html">SequenceEventType</A> type)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableSequenceEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceEvent">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html
new file mode 100644
index 0000000..f7dd16f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html
@@ -0,0 +1,246 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+VetoableSequenceListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="VetoableSequenceListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableSequenceListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.event</FONT>
+<BR>
+Interface VetoableSequenceListener</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.html">AbstractSequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.html">EmptySequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.htm [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>VetoableSequenceListener</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></DL>
+
+<P>
+VetoableSequenceListener.java
+
+ When a sequence wishes to change it should signal listeners of this
+ type first before it makes the change. If none of these listeners
+ veto the change, then it make occur after which listeners to type
+ SequenceChangeListener (including all of the
+ VetoableSequenceListeners ) should be signalled, at which
+ stage the change is unvetoable. Because there are two types of
+ listener it is not necessary to resignal the
+ VetoableSequenceListener's if a change is latter veto'd
+
+ Created: Tue Feb 15 19:28:56 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: VetoableSequenceListener.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ Method signalled before a prospective change occurs</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.event.SequenceListener"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD>Method signalled before a prospective change occurs
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE> - if the listener does not wish
+ the event to occur.</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="VetoableSequenceListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-frame.html
new file mode 100644
index 0000000..f9b8756
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-frame.html
@@ -0,0 +1,64 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.event()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.event()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.event</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceEventProvider.html" TARGET="classFrame"><I>SequenceEventProvider</I></A>
+<BR>
+<A HREF="SequenceListener.html" TARGET="classFrame"><I>SequenceListener</I></A>
+<BR>
+<A HREF="VetoableSequenceListener.html" TARGET="classFrame"><I>VetoableSequenceListener</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceEvent.html" TARGET="classFrame">SequenceEvent</A>
+<BR>
+<A HREF="SequenceEventType.html" TARGET="classFrame">SequenceEventType</A>
+<BR>
+<A HREF="SequenceListenerSupport.html" TARGET="classFrame">SequenceListenerSupport</A>
+<BR>
+<A HREF="VetoableSequenceEvent.html" TARGET="classFrame">VetoableSequenceEvent</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceVetoException.html" TARGET="classFrame">SequenceVetoException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-summary.html
new file mode 100644
index 0000000..0bdc1a4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-summary.html
@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.event()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.event()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.event
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceEventProvider.html"><I>SequenceEventProvider</I></A></B></TD>
+<TD>SequenceEventProvider.java
+
+ An interface designed to enforce the methods necessary to listen to a
+ sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceListener.html"><I>SequenceListener</I></A></B></TD>
+<TD>SequenceListener.java
+
+ Listens for events occuring to a sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VetoableSequenceListener.html"><I>VetoableSequenceListener</I></A></B></TD>
+<TD>VetoableSequenceListener.java
+
+ When a sequence wishes to change it should signal listeners of this
+ type first before it makes the change.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceEvent.html">SequenceEvent</A></B></TD>
+<TD>SequenceEvent.java
+
+ Instances of this class represent an event to a sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceEventType.html">SequenceEventType</A></B></TD>
+<TD>SequenceEventType.java
+
+ This class provides an enumerated type for the SequenceEvent class
+ to pass around as an identifier
+
+ Created: Tue Feb 15 20:10:48 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceListenerSupport.html">SequenceListenerSupport</A></B></TD>
+<TD>SequenceListenerSupport.java
+
+ This class provides support and handles the listeners to a specific
+ sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="VetoableSequenceEvent.html">VetoableSequenceEvent</A></B></TD>
+<TD>VetoableSequenceEvent.java
+
+
+ Created: Fri Feb 18 17:38:50 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceVetoException.html">SequenceVetoException</A></B></TD>
+<TD>SequenceVetoException.java
+
+ An exception thrown when an object vetos a sequence change event.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-tree.html
new file mode 100644
index 0000000..a75b2b0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/event/package-tree.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.event Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.event Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.event
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventType.html"><B>SequenceEventType</B></A></UL>
+<LI TYPE="circle">class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html"><B>EventObject</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html"><B>SequenceEvent</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html"><B>VetoableSequenceEvent</B></A></UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.html"><B>SequenceListenerSupport</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html"><B>SequenceVetoException</B></A></UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html"><B>EventListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html"><B>SequenceListener</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html"><B>VetoableSequenceListener</B></A></UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>SequenceEventProvider</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html
new file mode 100644
index 0000000..c744fad
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html
@@ -0,0 +1,427 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceAlignmentDimension
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignmentDimension";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentDimension.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.geom</FONT>
+<BR>
+Class SequenceAlignmentDimension</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceAlignmentDimension</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceAlignmentDimension.java
+
+ Represents a dimension within a SA. It is not a vast amount of use
+ without a point of reference (SequenceAlignmentPoint).
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignmentDimension.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><CODE>Created: Mon Mar 27 12:01:25 2000</CODE></A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#SequenceAlignmentDimension()">SequenceAlignmentDimension</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#SequenceAlignmentDimension(int, int)">SequenceAlignmentDimension</A></B>(int w,
+ int h)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#SequenceAlignmentDimension(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)">SequenceAlignmentDimension</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ Ascertains the equality of a given dimension to this
+ object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#getHeight()">getHeight</A></B>()</CODE>
+
+<BR>
+ Returns the height of this dimension.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#getSize()">getSize</A></B>()</CODE>
+
+<BR>
+ Returns the dimensions of this dimension (que????).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#getWidth()">getWidth</A></B>()</CODE>
+
+<BR>
+ Returns the width of this dimension.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#resize(int, int)">resize</A></B>(int w,
+ int h)</CODE>
+
+<BR>
+ Allows the resize of the dimension</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#setSize(int, int)">setSize</A></B>(int w,
+ int h)</CODE>
+
+<BR>
+ Sets the size of the dimension.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html#setSize(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)">setSize</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</CODE>
+
+<BR>
+ Sets the size of the dimension.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceAlignmentDimension()"><!-- --></A><H3>
+SequenceAlignmentDimension</H3>
+<PRE>
+public <B>SequenceAlignmentDimension</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentDimension(int, int)"><!-- --></A><H3>
+SequenceAlignmentDimension</H3>
+<PRE>
+public <B>SequenceAlignmentDimension</B>(int w,
+ int h)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentDimension(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><!-- --></A><H3>
+SequenceAlignmentDimension</H3>
+<PRE>
+public <B>SequenceAlignmentDimension</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
+equals</H3>
+<PRE>
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD>Ascertains the equality of a given dimension to this
+ object. Overrides the method in Object.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>obj</CODE> - the dimension
+<DT><B>Returns:</B><DD>the equality of the objects</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSize(int, int)"><!-- --></A><H3>
+setSize</H3>
+<PRE>
+public void <B>setSize</B>(int w,
+ int h)</PRE>
+<DL>
+<DD>Sets the size of the dimension. This method may further be
+ expanded if listeneers are appropriate, and to include any
+ necessary error checking.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>w</CODE> - the width of the dimension<DD><CODE>h</CODE> - the height of the dimension</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSize(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><!-- --></A><H3>
+setSize</H3>
+<PRE>
+public void <B>setSize</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</PRE>
+<DL>
+<DD>Sets the size of the dimension. This method will allow a
+ dimension to be duplicated. Calls setSize(int, int) to save on
+ correction procedures.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>dim</CODE> - a value of type 'SequenceAlignmentDimension'</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="resize(int, int)"><!-- --></A><H3>
+resize</H3>
+<PRE>
+public void <B>resize</B>(int w,
+ int h)</PRE>
+<DL>
+<DD>Allows the resize of the dimension
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>w</CODE> - the new width of the dimension<DD><CODE>h</CODE> - the new height of the dimension</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSize()"><!-- --></A><H3>
+getSize</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> <B>getSize</B>()</PRE>
+<DL>
+<DD>Returns the dimensions of this dimension (que????).
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the SA dimension</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getWidth()"><!-- --></A><H3>
+getWidth</H3>
+<PRE>
+public int <B>getWidth</B>()</PRE>
+<DL>
+<DD>Returns the width of this dimension.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the width</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getHeight()"><!-- --></A><H3>
+getHeight</H3>
+<PRE>
+public int <B>getHeight</B>()</PRE>
+<DL>
+<DD>Returns the height of this dimension.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the height</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentDimension.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html
new file mode 100644
index 0000000..82a2bec
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html
@@ -0,0 +1,571 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceAlignmentPoint
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignmentPoint";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentPoint.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.geom</FONT>
+<BR>
+Class SequenceAlignmentPoint</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Cloneable.html">Cloneable</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceAlignmentPoint</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Cloneable.html">Cloneable</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A></DL>
+
+<P>
+SequenceAlignmentPoint.java
+
+ Represents a point in an alignment, where X is the position in a
+ sequence, and Y is the index of the sequence in the alignment. No
+ checking is currently written into this object for the validity of
+ the point, and the opportunity to use listeners is not seized
+ (although this can easily be added later).
+
+ Created: Mon Mar 27 11:16:19 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignmentPoint.java,v 1.9 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#SequenceAlignmentPoint()">SequenceAlignmentPoint</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#SequenceAlignmentPoint(int, int)">SequenceAlignmentPoint</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#SequenceAlignmentPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">SequenceAlignmentPoint</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#clone()">clone</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#compareTo(java.lang.Object)">compareTo</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ Compares this point to another.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ Ascertains the equality of a given point to this
+ object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#getLocation()">getLocation</A></B>()</CODE>
+
+<BR>
+ Returns the location in the sequence alignment, represented by
+ this object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#getX()">getX</A></B>()</CODE>
+
+<BR>
+ Returns the X index of the point.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#getY()">getY</A></B>()</CODE>
+
+<BR>
+ Returns the Y index of the point.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#move(int, int)">move</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ Allows the moving of a point to a new position.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setLocation(int, int)">setLocation</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ Sets the location of the point.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setLocation(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">setLocation</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Sets the location of the point.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setX(int)">setX</A></B>(int x)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#setY(int)">setY</A></B>(int y)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#notify()">notify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.ht [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceAlignmentPoint()"><!-- --></A><H3>
+SequenceAlignmentPoint</H3>
+<PRE>
+public <B>SequenceAlignmentPoint</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentPoint(int, int)"><!-- --></A><H3>
+SequenceAlignmentPoint</H3>
+<PRE>
+public <B>SequenceAlignmentPoint</B>(int x,
+ int y)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentPoint(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+SequenceAlignmentPoint</H3>
+<PRE>
+public <B>SequenceAlignmentPoint</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
+equals</H3>
+<PRE>
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD>Ascertains the equality of a given point to this
+ object. Overrides the method in Object.
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>obj</CODE> - the point
+<DT><B>Returns:</B><DD>the equality of the objects</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="compareTo(java.lang.Object)"><!-- --></A><H3>
+compareTo</H3>
+<PRE>
+public int <B>compareTo</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD>Compares this point to another. Points are compared by comparing
+ first the value of getX(), and then getY(). If obj is not a
+ SequenceAlignmentPoint an exception is thrown.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>compareTo</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setX(int)"><!-- --></A><H3>
+setX</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>setX</B>(int x)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setY(int)"><!-- --></A><H3>
+setY</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>setY</B>(int y)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setLocation(int, int)"><!-- --></A><H3>
+setLocation</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>setLocation</B>(int x,
+ int y)</PRE>
+<DL>
+<DD>Sets the location of the point. This method can be further
+ expanded if listeners are appropriate, and to include error
+ checking.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the x position of the point<DD><CODE>y</CODE> - the y position of the point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setLocation(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+setLocation</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>setLocation</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Sets the location of the point. This method will allow a point to
+ be duplicated. Calls setLocation(int, int) to save on correction
+ procedures.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point in a sequence alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="move(int, int)"><!-- --></A><H3>
+move</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>move</B>(int x,
+ int y)</PRE>
+<DL>
+<DD>Allows the moving of a point to a new position.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the X index<DD><CODE>y</CODE> - the Y index</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLocation()"><!-- --></A><H3>
+getLocation</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getLocation</B>()</PRE>
+<DL>
+<DD>Returns the location in the sequence alignment, represented by
+ this object.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the location represented by this point</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getX()"><!-- --></A><H3>
+getX</H3>
+<PRE>
+public int <B>getX</B>()</PRE>
+<DL>
+<DD>Returns the X index of the point.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the X index</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getY()"><!-- --></A><H3>
+getY</H3>
+<PRE>
+public int <B>getY</B>()</PRE>
+<DL>
+<DD>Returns the Y index of the point.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the Y index</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clone()"><!-- --></A><H3>
+clone</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>clone</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/CloneNotSupportedException.html">CloneNotSupportedException</A></PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/CloneNotSupportedException.html">CloneNotSupportedException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentPoint.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html
new file mode 100644
index 0000000..23b2b08
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html
@@ -0,0 +1,830 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceAlignmentRectangle
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignmentRectangle";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentRectangle.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.geom</FONT>
+<BR>
+Class SequenceAlignmentRectangle</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceAlignmentRectangle</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A></DL>
+
+<P>
+SequenceAlignmentRectangle.java
+
+ Defines a rectangular region in a sequence alignment. NB: objects
+ of this class perform no checks as to the validity of the region
+ defined.
+
+ Created: Mon Mar 27 12:41:18 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignmentRectangle.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle()">SequenceAlignmentRectangle</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(int, int, int, int)">SequenceAlignmentRectangle</A></B>(int x,
+ int y,
+ int width,
+ int height)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(int, int, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)">SequenceAlignmentRectangle</A></B>(int x,
+ int y,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int, int)">SequenceAlignmentRectangle</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ int width,
+ int height)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#SequenceAlignmentRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">SequenceAlignmentRectangle</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#add(int, int)">add</A></B>(int newx,
+ int newy)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#add(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">add</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#compareTo(java.lang.Object)">compareTo</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ Compares another rectangle to this one.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#contains(int, int)">contains</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ Determines whether a point is contained in this region.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#contains(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">contains</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Determines whether a point is contained in this region.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</CODE>
+
+<BR>
+ Compares two SARectangles for equality (ie: whether they have the
+ same dimension and location).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getBounds()">getBounds</A></B>()</CODE>
+
+<BR>
+ Returns the rectangle which defines the boundries of the region
+ defined by this object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getHeight()">getHeight</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getLocation()">getLocation</A></B>()</CODE>
+
+<BR>
+ Returns the location of the rectangle</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getSize()">getSize</A></B>()</CODE>
+
+<BR>
+ Returns the size of the rectangle.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getWidth()">getWidth</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getX()">getX</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#getY()">getY</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setBounds(int, int, int, int)">setBounds</A></B>(int x,
+ int y,
+ int width,
+ int height)</CODE>
+
+<BR>
+ Sets the boundry defined by this region.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)">setBounds</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</CODE>
+
+<BR>
+ Sets the boundry defined by this region.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">setBounds</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ Sets the boundry defined by this region.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setLocation(int, int)">setLocation</A></B>(int x,
+ int y)</CODE>
+
+<BR>
+ Sets the progom location of the rectangle.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setLocation(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)">setLocation</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</CODE>
+
+<BR>
+ Sets the origin location of the rectangle.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setSize(int, int)">setSize</A></B>(int width,
+ int height)</CODE>
+
+<BR>
+ Sets the size of the rectangle.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#setSize(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)">setSize</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</CODE>
+
+<BR>
+ Sets the size of the rectangle.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceAlignmentRectangle()"><!-- --></A><H3>
+SequenceAlignmentRectangle</H3>
+<PRE>
+public <B>SequenceAlignmentRectangle</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentRectangle(int, int, int, int)"><!-- --></A><H3>
+SequenceAlignmentRectangle</H3>
+<PRE>
+public <B>SequenceAlignmentRectangle</B>(int x,
+ int y,
+ int width,
+ int height)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+SequenceAlignmentRectangle</H3>
+<PRE>
+public <B>SequenceAlignmentRectangle</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentRectangle(int, int, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><!-- --></A><H3>
+SequenceAlignmentRectangle</H3>
+<PRE>
+public <B>SequenceAlignmentRectangle</B>(int x,
+ int y,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SequenceAlignmentRectangle(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, int, int)"><!-- --></A><H3>
+SequenceAlignmentRectangle</H3>
+<PRE>
+public <B>SequenceAlignmentRectangle</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ int width,
+ int height)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="contains(int, int)"><!-- --></A><H3>
+contains</H3>
+<PRE>
+public boolean <B>contains</B>(int x,
+ int y)</PRE>
+<DL>
+<DD>Determines whether a point is contained in this region.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the position in the sequence<DD><CODE>y</CODE> - the sequence index in the alignment
+<DT><B>Returns:</B><DD>whether a point is contained in this region</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="contains(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+contains</H3>
+<PRE>
+public boolean <B>contains</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Determines whether a point is contained in this region.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the point
+<DT><B>Returns:</B><DD>whether a point is contained in this region</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
+equals</H3>
+<PRE>
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD>Compares two SARectangles for equality (ie: whether they have the
+ same dimension and location).
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>obj</CODE> - the SARectangle for comparison
+<DT><B>Returns:</B><DD>the equality of the objects</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="compareTo(java.lang.Object)"><!-- --></A><H3>
+compareTo</H3>
+<PRE>
+public int <B>compareTo</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> obj)</PRE>
+<DL>
+<DD>Compares another rectangle to this one. Comparison is done by
+ comparing the location point. If this is equal then the width,
+ then the height are compared. Throws a class cast if obj is
+ not a SequenceAlignmentRectangle
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>compareTo</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setBounds(int, int, int, int)"><!-- --></A><H3>
+setBounds</H3>
+<PRE>
+public void <B>setBounds</B>(int x,
+ int y,
+ int width,
+ int height)</PRE>
+<DL>
+<DD>Sets the boundry defined by this region.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the position in the sequence<DD><CODE>y</CODE> - the sequence index in the alignment<DD><CODE>width</CODE> - the width of the SARectangle<DD><CODE>height</CODE> - the height of the SARectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint, uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><!-- --></A><H3>
+setBounds</H3>
+<PRE>
+public void <B>setBounds</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</PRE>
+<DL>
+<DD>Sets the boundry defined by this region.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the origin location of the new SARectangle<DD><CODE>dim</CODE> - the size of the new SARectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setBounds(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+setBounds</H3>
+<PRE>
+public void <B>setBounds</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD>Sets the boundry defined by this region.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>rect</CODE> - the rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getBounds()"><!-- --></A><H3>
+getBounds</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getBounds</B>()</PRE>
+<DL>
+<DD>Returns the rectangle which defines the boundries of the region
+ defined by this object.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html#getBounds()">getBounds</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the rectangle<DT><B>See Also:</B><DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html"><CODE>SequenceAlignmentShape</CODE></A></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setLocation(int, int)"><!-- --></A><H3>
+setLocation</H3>
+<PRE>
+public void <B>setLocation</B>(int x,
+ int y)</PRE>
+<DL>
+<DD>Sets the progom location of the rectangle. X corresponds to the
+ position in the sequence, and Y corresponds to the index of the
+ sequence in the alignment.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>x</CODE> - the new X location of the rectangle<DD><CODE>y</CODE> - the new Y location of the rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setLocation(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+setLocation</H3>
+<PRE>
+public void <B>setLocation</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD>Sets the origin location of the rectangle.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>point</CODE> - the new location</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLocation()"><!-- --></A><H3>
+getLocation</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> <B>getLocation</B>()</PRE>
+<DL>
+<DD>Returns the location of the rectangle
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the location</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSize(int, int)"><!-- --></A><H3>
+setSize</H3>
+<PRE>
+public void <B>setSize</B>(int width,
+ int height)</PRE>
+<DL>
+<DD>Sets the size of the rectangle.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>width</CODE> - the width of the new rectangle<DD><CODE>height</CODE> - the height of the new rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSize(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentDimension)"><!-- --></A><H3>
+setSize</H3>
+<PRE>
+public void <B>setSize</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> dim)</PRE>
+<DL>
+<DD>Sets the size of the rectangle.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>dim</CODE> - the new dimension</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSize()"><!-- --></A><H3>
+getSize</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html">SequenceAlignmentDimension</A> <B>getSize</B>()</PRE>
+<DL>
+<DD>Returns the size of the rectangle.
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the dimensions of the rectangle</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getX()"><!-- --></A><H3>
+getX</H3>
+<PRE>
+public int <B>getX</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getY()"><!-- --></A><H3>
+getY</H3>
+<PRE>
+public int <B>getY</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getHeight()"><!-- --></A><H3>
+getHeight</H3>
+<PRE>
+public int <B>getHeight</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getWidth()"><!-- --></A><H3>
+getWidth</H3>
+<PRE>
+public int <B>getWidth</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="add(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public void <B>add</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html">SequenceAlignmentPoint</A> point)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="add(int, int)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public void <B>add</B>(int newx,
+ int newy)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentRectangle.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html
new file mode 100644
index 0000000..67b5540
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:31 BST 2002 -->
+<TITLE>
+SequenceAlignmentShape
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignmentShape";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentShape.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.geom</FONT>
+<BR>
+Interface SequenceAlignmentShape</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceAlignmentShape</B></DL>
+
+<P>
+SequenceAlignmentShape.java
+
+ Defines a shape used to identify a region in a sequence alignment.
+
+ Created: Mon Mar 27 12:38:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignmentShape.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html#getBounds()">getBounds</A></B>()</CODE>
+
+<BR>
+ Returns the boundaries of the shape used to identify a region in
+ a sequence alignment.</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getBounds()"><!-- --></A><H3>
+getBounds</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> <B>getBounds</B>()</PRE>
+<DL>
+<DD>Returns the boundaries of the shape used to identify a region in
+ a sequence alignment.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the rectangle that defines the boundries</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentShape.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-frame.html
new file mode 100644
index 0000000..3510f1d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-frame.html
@@ -0,0 +1,47 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.geom()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.geom()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.geom</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceAlignmentShape.html" TARGET="classFrame"><I>SequenceAlignmentShape</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="SequenceAlignmentDimension.html" TARGET="classFrame">SequenceAlignmentDimension</A>
+<BR>
+<A HREF="SequenceAlignmentPoint.html" TARGET="classFrame">SequenceAlignmentPoint</A>
+<BR>
+<A HREF="SequenceAlignmentRectangle.html" TARGET="classFrame">SequenceAlignmentRectangle</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-summary.html
new file mode 100644
index 0000000..26ded8e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-summary.html
@@ -0,0 +1,165 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.geom()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.geom()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.geom
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignmentShape.html"><I>SequenceAlignmentShape</I></A></B></TD>
+<TD>SequenceAlignmentShape.java
+
+ Defines a shape used to identify a region in a sequence alignment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignmentDimension.html">SequenceAlignmentDimension</A></B></TD>
+<TD>SequenceAlignmentDimension.java
+
+ Represents a dimension within a SA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignmentPoint.html">SequenceAlignmentPoint</A></B></TD>
+<TD>SequenceAlignmentPoint.java
+
+ Represents a point in an alignment, where X is the position in a
+ sequence, and Y is the index of the sequence in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A></B></TD>
+<TD>SequenceAlignmentRectangle.java
+
+ Defines a rectangular region in a sequence alignment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-tree.html
new file mode 100644
index 0000000..feb6c77
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/geom/package-tree.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.geom Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.geom Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.geom
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.geom.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.html"><B>SequenceAlignmentDimension</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.geom.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.html"><B>SequenceAlignmentPoint</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Cloneable.html">Cloneable</A>, java.lang.<A HR [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.geom.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html"><B>SequenceAlignmentRectangle</B></A> (implements java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Comparable.html">Comparable</A>, uk.ac.man.bioinf.sequence.geom.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html">SequenceAlignmentShape</A>)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.geom.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.html"><B>SequenceAlignmentShape</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html
new file mode 100644
index 0000000..8383e1e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html
@@ -0,0 +1,278 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+AbstractGappedSequenceGroup
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractGappedSequenceGroup";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractGappedSequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.group</FONT>
+<BR>
+Class AbstractGappedSequenceGroup</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html">GroupSequenceAlignment</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractGappedSequenceGroup</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A></DL>
+
+<P>
+AbstractGappedSequenceGroup.java
+
+
+ Created: Thu Jun 1 18:25:15 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractGappedSequenceGroup.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#AbstractGappedSequenceGroup()">AbstractGappedSequenceGroup</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#getGappedSequences()">getGappedSequences</A></B>()</CODE>
+
+<BR>
+ Return all the sequences in this group as a GappedSequence
+ array.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.group.SequenceGroup"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)">addSequenceToGroup</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#clearSequences()">clearSequences</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)">containsSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/g [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractGappedSequenceGroup()"><!-- --></A><H3>
+AbstractGappedSequenceGroup</H3>
+<PRE>
+public <B>AbstractGappedSequenceGroup</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getGappedSequences()"><!-- --></A><H3>
+getGappedSequences</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] <B>getGappedSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A></CODE></B></DD>
+<DD>Return all the sequences in this group as a GappedSequence
+ array. If this group contains sequences which are not
+ GappedSequences this will result in a run time
+ ClassCastException
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html#getGappedSequences()">getGappedSequences</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequences</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractGappedSequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html
new file mode 100644
index 0000000..86a712d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html
@@ -0,0 +1,444 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+DefaultGappedSequenceGroup
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DefaultGappedSequenceGroup";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultGappedSequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.group</FONT>
+<BR>
+Class DefaultGappedSequenceGroup</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.group.DefaultGappedSequenceGroup</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DefaultGappedSequenceGroup</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></DL>
+
+<P>
+DefaultGappedSequenceGroup.java
+
+
+ Created: Thu Jun 1 18:33:14 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DefaultGappedSequenceGroup.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#DefaultGappedSequenceGroup()">DefaultGappedSequenceGroup</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)">addSequenceToGroup</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ Adds a sequence to this group</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#clearSequences()">clearSequences</A></B>()</CODE>
+
+<BR>
+ Empty the group of sequences</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)">containsSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ Does this group contain the sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getGappedSequenceAt(int)">getGappedSequenceAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getNumberSequences()">getNumberSequences</A></B>()</CODE>
+
+<BR>
+ Return the number of sequences in this group.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getSequenceAt(int)">getSequenceAt</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#getSequences()">getSequences</A></B>()</CODE>
+
+<BR>
+ Get all the sequences in this group.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#iterator()">iterator</A></B>()</CODE>
+
+<BR>
+ Returns an iterator of all the sequences.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)">removeSequenceFromGroup</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ Removes a sequence from this group</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#getGappedSequences()">getGappedSequences</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DefaultGappedSequenceGroup()"><!-- --></A><H3>
+DefaultGappedSequenceGroup</H3>
+<PRE>
+public <B>DefaultGappedSequenceGroup</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+addSequenceToGroup</H3>
+<PRE>
+public void <B>addSequenceToGroup</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Adds a sequence to this group
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+removeSequenceFromGroup</H3>
+<PRE>
+public void <B>removeSequenceFromGroup</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Removes a sequence from this group
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="containsSequence(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+containsSequence</H3>
+<PRE>
+public boolean <B>containsSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Does this group contain the sequence
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence
+<DT><B>Returns:</B><DD>true if containined</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequences()"><!-- --></A><H3>
+getSequences</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>[] <B>getSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Get all the sequences in this group.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSequences()"><!-- --></A><H3>
+clearSequences</H3>
+<PRE>
+public void <B>clearSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Empty the group of sequences
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSequences()"><!-- --></A><H3>
+getNumberSequences</H3>
+<PRE>
+public int <B>getNumberSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Return the number of sequences in this group.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAt(int)"><!-- --></A><H3>
+getSequenceAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> <B>getSequenceAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getGappedSequenceAt(int)"><!-- --></A><H3>
+getGappedSequenceAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getGappedSequenceAt</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="iterator()"><!-- --></A><H3>
+iterator</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A> <B>iterator</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Returns an iterator of all the sequences. This should be fail
+ fast if the group is modified whilst the iterator is being used.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DefaultGappedSequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html
new file mode 100644
index 0000000..9c7d384
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html
@@ -0,0 +1,237 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+GappedSequenceGroup
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappedSequenceGroup";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.group</FONT>
+<BR>
+Interface GappedSequenceGroup</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>GappedSequenceGroup</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></DL>
+
+<P>
+GappedSequenceGroup.java
+
+ An extension of SequenceGroup with some methods to return
+ GappedSequences.
+ Created: Thu Jun 1 18:17:54 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappedSequenceGroup.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html#getGappedSequences()">getGappedSequences</A></B>()</CODE>
+
+<BR>
+ Return all the sequences in this group as a GappedSequence
+ array.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.group.SequenceGroup"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)">addSequenceToGroup</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#clearSequences()">clearSequences</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)">containsSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/g [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getGappedSequences()"><!-- --></A><H3>
+getGappedSequences</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>[] <B>getGappedSequences</B>()</PRE>
+<DL>
+<DD>Return all the sequences in this group as a GappedSequence
+ array. If this group contains sequences which are not
+ GappedSequences this will result in a run time
+ ClassCastException
+<P>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequences</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html
new file mode 100644
index 0000000..3cb5f0d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html
@@ -0,0 +1,1071 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+GroupSequenceAlignment
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GroupSequenceAlignment";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GroupSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.group</FONT>
+<BR>
+Class GroupSequenceAlignment</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGrou [...]
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.html">CinemaGroup</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>GroupSequenceAlignment</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></DL>
+
+<P>
+GroupSequenceAlignment.java
+
+ This is a sequence group which also reflects a sequence
+ alignment. The sequences will be given out in the same order, as
+ they are in the SequenceAlignment. A given group is linked
+ specifically to a single SequenceAlignment. If sequences are
+ removed from the SequenceAlignment then they are automatically
+ removed from this class.
+
+ Created: Thu Jun 1 23:20:37 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GroupSequenceAlignment.java,v 1.9 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#GroupSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">GroupSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ Start an empty sequence group associated with the given sequence
+ alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#GroupSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.util.IntArrayList)">GroupSequenceAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> seqArray)</CODE>
+
+<BR>
+ Starts an Sequence group with the sequences given in the IntArrayList</TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Add a listener specifically interested in events connected with the MSA.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)</CODE>
+
+<BR>
+ Adds a sequence to the current alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)">addSequenceToGroup</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</CODE>
+
+<BR>
+ Adds a sequence to this group.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Adds a listener interested in vetoing multiple sequence alignment
+ specific events.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Adds the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#clearSequences()">clearSequences</A></B>()</CODE>
+
+<BR>
+ Empty the group of sequences</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)">containsSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</CODE>
+
+<BR>
+ Does this group contain the sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getInset(int)">getInset</A></B>(int index)</CODE>
+
+<BR>
+ Returns the inset of sequence within the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getLength()">getLength</A></B>()</CODE>
+
+<BR>
+ Returns the length of the alignment (i.e: the longest sequence).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getNumberSequences()">getNumberSequences</A></B>()</CODE>
+
+<BR>
+ Returns the total number of sequences in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequenceAt(int)">getSequenceAt</A></B>(int index)</CODE>
+
+<BR>
+ Provides the sequence at a particular location in the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceIndex</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> sequence)</CODE>
+
+<BR>
+ Returns the index in the alignment of a provided sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequences()">getSequences</A></B>()</CODE>
+
+<BR>
+ Get all the sequences in this group.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSequenceType()">getSequenceType</A></B>()</CODE>
+
+<BR>
+ Returns the sequence type of the alignment (e.g: protein sequences).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSubAlignment(int, int, int, int)">getSubAlignment</A></B>(int startPos,
+ int endPos,
+ int startSeq,
+ int endSeq)</CODE>
+
+<BR>
+ Returns a sub-alignment, given the exact location in this alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#iterator()">iterator</A></B>()</CODE>
+
+<BR>
+ Returns an iterator of all the sequences.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeSequence(int)">removeSequence</A></B>(int seqIndex)</CODE>
+
+<BR>
+ Removes a sequence from the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)">removeSequenceFromGroup</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</CODE>
+
+<BR>
+ Removes a sequence from this group</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</CODE>
+
+<BR>
+ Removes a vetoable multiple sequence alignment listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</CODE>
+
+<BR>
+ Removes the specified vetoable sequence listener.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#setInset(int, int)">setInset</A></B>(int seqIndex,
+ int size)</CODE>
+
+<BR>
+ Sets the inset of a sequence within the alignment.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ Method signalled before a prospective change occurs</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.group.AbstractGappedSequenceGroup"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html#getGappedSequences()">getGappedSequences</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GroupSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+GroupSequenceAlignment</H3>
+<PRE>
+public <B>GroupSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+<DD>Start an empty sequence group associated with the given sequence
+ alignment.
+<P>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> - the alignment</DL>
+<HR>
+
+<A NAME="GroupSequenceAlignment(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment, uk.ac.man.bioinf.util.IntArrayList)"><!-- --></A><H3>
+GroupSequenceAlignment</H3>
+<PRE>
+public <B>GroupSequenceAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment,
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> seqArray)</PRE>
+<DL>
+<DD>Starts an Sequence group with the sequences given in the IntArrayList
+<P>
+<DT><B>Parameters:</B><DD><CODE>alignment</CODE> - <DD><CODE>seqArray</CODE> - </DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSequences()"><!-- --></A><H3>
+getSequences</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>[] <B>getSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Get all the sequences in this group.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#getSequences()">getSequences</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+addSequenceToGroup</H3>
+<PRE>
+public void <B>addSequenceToGroup</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</PRE>
+<DL>
+<DD>Adds a sequence to this group.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)">addSequenceToGroup</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></CODE> - if this sequence is not part of
+ the associated SequenceAlignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)"><!-- --></A><H3>
+addSequence</H3>
+<PRE>
+public void <B>addSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq,
+ int inset)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Adds a sequence to the current alignment. If listeners are
+ listening to the alignment, they will be able to veto the add
+ (thats the idea atleast).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#addSequence(uk.ac.man.bioinf.sequence.alignment.GappedSequence, int)">addSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence to be added<DD><CODE>inset</CODE> - the sequence inset
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getLength()"><!-- --></A><H3>
+getLength</H3>
+<PRE>
+public int <B>getLength</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the length of the alignment (i.e: the longest sequence).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getLength()">getLength</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>length of alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+removeSequenceFromGroup</H3>
+<PRE>
+public void <B>removeSequenceFromGroup</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Removes a sequence from this group
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)">removeSequenceFromGroup</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequence(int)"><!-- --></A><H3>
+removeSequence</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>removeSequence</B>(int seqIndex)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Removes a sequence from the alignment. It requires the knowledge
+ of the sequence location in the alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#removeSequence(int)">removeSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the index of the sequence
+<DT><B>Returns:</B><DD>the sequence
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setInset(int, int)"><!-- --></A><H3>
+setInset</H3>
+<PRE>
+public void <B>setInset</B>(int seqIndex,
+ int size)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Sets the inset of a sequence within the alignment. An inset of
+ zero will mean that the first element starts at the left most
+ position of the alignment.
+ <p>
+ Special N.B.: This was put into the interface because it was
+ felt that there would not be any instances when you would not
+ wish to do this (apart from a read-only alignment, in which case
+ there are ways and means).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#setInset(int, int)">setInset</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seqIndex</CODE> - the index of the sequence<DD><CODE>size</CODE> - the size of the inset
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSequences()"><!-- --></A><H3>
+clearSequences</H3>
+<PRE>
+public void <B>clearSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Empty the group of sequences
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#clearSequences()">clearSequences</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSequences()"><!-- --></A><H3>
+getNumberSequences</H3>
+<PRE>
+public int <B>getNumberSequences</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the total number of sequences in the alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getNumberSequences()">getNumberSequences</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of sequences</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="containsSequence(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+containsSequence</H3>
+<PRE>
+public boolean <B>containsSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> sequence)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Does this group contain the sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)">containsSequence</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the sequence
+<DT><B>Returns:</B><DD>true if containined</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="iterator()"><!-- --></A><H3>
+iterator</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A> <B>iterator</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></B></DD>
+<DD>Returns an iterator of all the sequences. This should be fail
+ fast if the group is modified whilst the iterator is being used.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#iterator()">iterator</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html">SequenceGroup</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceAt(int)"><!-- --></A><H3>
+getSequenceAt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> <B>getSequenceAt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Provides the sequence at a particular location in the alignment.
+ The indexing STARTS AT 1, and not 0.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceAt(int)">getSequenceAt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the index of the target sequence
+<DT><B>Returns:</B><DD>the sequence of interest</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(int, int, int, int)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(int startPos,
+ int endPos,
+ int startSeq,
+ int endSeq)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns a sub-alignment, given the exact location in this alignment.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(int, int, int, int)">getSubAlignment</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>startPos</CODE> - the start position for the sub-alignment (i.e: x1)<DD><CODE>endPos</CODE> - the length of the sub alignment<DD><CODE>startSeq</CODE> - the first sequence in the current alignment to be
+ included in the sub-alignment (i.e: y1)
+<DT><B>Returns:</B><DD>the sub-alignment</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)"><!-- --></A><H3>
+getSubAlignment</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> <B>getSubAlignment</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.html">SequenceAlignmentRectangle</A> rect)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSubAlignment(uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle)">getSubAlignment</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceType()"><!-- --></A><H3>
+getSequenceType</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getSequenceType</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the sequence type of the alignment (e.g: protein sequences).
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceType()">getSequenceType</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the sequence type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getInset(int)"><!-- --></A><H3>
+getInset</H3>
+<PRE>
+public int <B>getInset</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the inset of sequence within the alignment.
+ A inset of 0 means that the first element means that the Sequence
+ starts at the left most position of the alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getInset(int)">getInset</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - the sequence index
+<DT><B>Returns:</B><DD>the inset or preceeding number of gaps</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+getSequenceIndex</H3>
+<PRE>
+public int <B>getSequenceIndex</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> sequence)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></B></DD>
+<DD>Returns the index in the alignment of a provided sequence.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html#getSequenceIndex(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">getSequenceIndex</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - the query sequence
+<DT><B>Returns:</B><DD>the index of the sequence, or -1 if not found</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+removeAlignmentListener</H3>
+<PRE>
+public void <B>removeAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">removeAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)"><!-- --></A><H3>
+addAlignmentListener</H3>
+<PRE>
+public void <B>addAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Add a listener specifically interested in events connected with the MSA.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener)">addAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+removeVetoableAlignmentListener</H3>
+<PRE>
+public void <B>removeVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Removes a vetoable multiple sequence alignment listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#removeVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">removeVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the listener to be removed</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)"><!-- --></A><H3>
+addVetoableAlignmentListener</H3>
+<PRE>
+public void <B>addVetoableAlignmentListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></B></DD>
+<DD>Adds a listener interested in vetoing multiple sequence alignment
+ specific events.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html#addVetoableAlignmentListener(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener)">addVetoableAlignmentListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.html">AlignmentEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - a vetoable multiple sequence alignment listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></B></DD>
+<DD>Method signalled before a prospective change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE> - if the listener does not wish
+ the event to occur.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+addSequenceListener</H3>
+<PRE>
+public void <B>addSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">addSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)"><!-- --></A><H3>
+removeSequenceListener</H3>
+<PRE>
+public void <B>removeSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeSequenceListener(uk.ac.man.bioinf.sequence.event.SequenceListener)">removeSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+addVetoableSequenceListener</H3>
+<PRE>
+public void <B>addVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Adds the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#addVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">addVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)"><!-- --></A><H3>
+removeVetoableSequenceListener</H3>
+<PRE>
+public void <B>removeVetoableSequenceListener</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A> listener)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></B></DD>
+<DD>Removes the specified vetoable sequence listener.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html#removeVetoableSequenceListener(uk.ac.man.bioinf.sequence.event.VetoableSequenceListener)">removeVetoableSequenceListener</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>listener</CODE> - the vetoable sequence listener</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html">Identifiable</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GroupSequenceAlignment.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/SequenceGroup.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/SequenceGroup.html
new file mode 100644
index 0000000..abf365a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/SequenceGroup.html
@@ -0,0 +1,355 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:30 BST 2002 -->
+<TITLE>
+SequenceGroup
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceGroup";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.group</FONT>
+<BR>
+Interface SequenceGroup</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceGroup</B></DL>
+
+<P>
+SequenceGroup.java
+
+ This interface defines a SequenceGroup that is capable of storing a
+ collection of sequences. It would usually be expected that the
+ sequences in the group would usually have something in common with
+ each other, being for instance some of the members of a
+ SequenceAlignment, although this is not required.
+
+ Created: Thu Jun 1 18:09:32 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceGroup.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)">addSequenceToGroup</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ Adds a sequence to this group</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#clearSequences()">clearSequences</A></B>()</CODE>
+
+<BR>
+ Empty the group of sequences</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#containsSequence(uk.ac.man.bioinf.sequence.Sequence)">containsSequence</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ Does this group contain the sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#getNumberSequences()">getNumberSequences</A></B>()</CODE>
+
+<BR>
+ Return the number of sequences in this group.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#getSequences()">getSequences</A></B>()</CODE>
+
+<BR>
+ Get all the sequences in this group.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#iterator()">iterator</A></B>()</CODE>
+
+<BR>
+ Returns an iterator of all the sequences.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html#removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)">removeSequenceFromGroup</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ Removes a sequence from this group</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addSequenceToGroup(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+addSequenceToGroup</H3>
+<PRE>
+public void <B>addSequenceToGroup</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD>Adds a sequence to this group
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeSequenceFromGroup(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+removeSequenceFromGroup</H3>
+<PRE>
+public void <B>removeSequenceFromGroup</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD>Removes a sequence from this group
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="containsSequence(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+containsSequence</H3>
+<PRE>
+public boolean <B>containsSequence</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD>Does this group contain the sequence
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>seq</CODE> - the sequence
+<DT><B>Returns:</B><DD>true if containined</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSequences()"><!-- --></A><H3>
+getSequences</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>[] <B>getSequences</B>()</PRE>
+<DL>
+<DD>Get all the sequences in this group.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clearSequences()"><!-- --></A><H3>
+clearSequences</H3>
+<PRE>
+public void <B>clearSequences</B>()</PRE>
+<DL>
+<DD>Empty the group of sequences
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getNumberSequences()"><!-- --></A><H3>
+getNumberSequences</H3>
+<PRE>
+public int <B>getNumberSequences</B>()</PRE>
+<DL>
+<DD>Return the number of sequences in this group.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="iterator()"><!-- --></A><H3>
+iterator</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A> <B>iterator</B>()</PRE>
+<DL>
+<DD>Returns an iterator of all the sequences. This should be fail
+ fast if the group is modified whilst the iterator is being used.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceGroup.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-frame.html
new file mode 100644
index 0000000..b99cb08
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-frame.html
@@ -0,0 +1,49 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.group()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.group()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.group</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="GappedSequenceGroup.html" TARGET="classFrame"><I>GappedSequenceGroup</I></A>
+<BR>
+<A HREF="SequenceGroup.html" TARGET="classFrame"><I>SequenceGroup</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractGappedSequenceGroup.html" TARGET="classFrame">AbstractGappedSequenceGroup</A>
+<BR>
+<A HREF="DefaultGappedSequenceGroup.html" TARGET="classFrame">DefaultGappedSequenceGroup</A>
+<BR>
+<A HREF="GroupSequenceAlignment.html" TARGET="classFrame">GroupSequenceAlignment</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-summary.html
new file mode 100644
index 0000000..89d998a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-summary.html
@@ -0,0 +1,175 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.group()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.group()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.group
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappedSequenceGroup.html"><I>GappedSequenceGroup</I></A></B></TD>
+<TD>GappedSequenceGroup.java
+
+ An extension of SequenceGroup with some methods to return
+ GappedSequences.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceGroup.html"><I>SequenceGroup</I></A></B></TD>
+<TD>SequenceGroup.java
+
+ This interface defines a SequenceGroup that is capable of storing a
+ collection of sequences.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractGappedSequenceGroup.html">AbstractGappedSequenceGroup</A></B></TD>
+<TD>AbstractGappedSequenceGroup.java
+
+
+ Created: Thu Jun 1 18:25:15 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultGappedSequenceGroup.html">DefaultGappedSequenceGroup</A></B></TD>
+<TD>DefaultGappedSequenceGroup.java
+
+
+ Created: Thu Jun 1 18:33:14 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GroupSequenceAlignment.html">GroupSequenceAlignment</A></B></TD>
+<TD>GroupSequenceAlignment.java
+
+ This is a sequence group which also reflects a sequence
+ alignment.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-tree.html
new file mode 100644
index 0000000..9bef441
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/group/package-tree.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.group Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.group Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.group
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.html"><B>AbstractGappedSequenceGroup</B></A> (implements uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html">GappedSequenceGroup</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.html"><B>DefaultGappedSequenceGroup</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.html"><B>GroupSequenceAlignment</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/Alignm [...]
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/SequenceGroup.html"><B>SequenceGroup</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.group.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.html"><B>GappedSequenceGroup</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/geom/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html
new file mode 100644
index 0000000..d00e715
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+AbstractIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class AbstractIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.html">ConsensusIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html">SimpleIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractIdentifier</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DL>
+
+<P>
+AbstractSequenceIdentifier.java
+
+
+ Created: Wed Jul 5 16:00:43 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractIdentifier.java,v 1.3 2001/05/24 15:36:13 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#AbstractIdentifier(uk.ac.man.bioinf.sequence.identifier.Source)">AbstractIdentifier</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#getSource()">getSource</A></B>()</CODE>
+
+<BR>
+ This returns the source of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.Identifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#getTitle()">getTitle</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractIdentifier(uk.ac.man.bioinf.sequence.identifier.Source)"><!-- --></A><H3>
+AbstractIdentifier</H3>
+<PRE>
+public <B>AbstractIdentifier</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSource()"><!-- --></A><H3>
+getSource</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> <B>getSource</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></B></DD>
+<DD>This returns the source of the sequence. This might be a File
+ object if the sequence has been read straight from file, or a URL
+ from the internet. Alternatively it could be a Java Obect
+ reference if the sequence has been retrieved by calculation, say
+ of a Consensus.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#getSource()">getSource</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSource(uk.ac.man.bioinf.sequence.identifier.Source)"><!-- --></A><H3>
+setSource</H3>
+<PRE>
+public void <B>setSource</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html
new file mode 100644
index 0000000..a45cd59
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html
@@ -0,0 +1,313 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+DatabaseIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DatabaseIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DatabaseIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class DatabaseIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html">SwissProtIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>DatabaseIdentifier</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></DL>
+
+<P>
+DatabaseIdentifier.java
+
+
+ Created: Wed Jul 5 14:11:46 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DatabaseIdentifier.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#DatabaseIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, java.lang.String)">DatabaseIdentifier</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accession)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getAccession()">getAccession</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getDatabaseName()">getDatabaseName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Gets a human readable title for the Sequence</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#getSource()">getSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="DatabaseIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, java.lang.String)"><!-- --></A><H3>
+DatabaseIdentifier</H3>
+<PRE>
+public <B>DatabaseIdentifier</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accession)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getAccession()"><!-- --></A><H3>
+getAccession</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getAccession</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getDatabaseName()"><!-- --></A><H3>
+getDatabaseName</H3>
+<PRE>
+public abstract <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDatabaseName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></B></DD>
+<DD>Gets a human readable title for the Sequence
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DatabaseIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/FileSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/FileSource.html
new file mode 100644
index 0000000..352d7d2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/FileSource.html
@@ -0,0 +1,284 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+FileSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="FileSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class FileSource</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.FileSource</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>FileSource</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DL>
+
+<P>
+FileSource.java
+
+
+ Created: Fri Sep 8 18:57:27 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: FileSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html#FileSource(java.io.File)">FileSource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html#getFile()">getFile</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Get the human readable name for this SequenceSource</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="FileSource(java.io.File)"><!-- --></A><H3>
+FileSource</H3>
+<PRE>
+public <B>FileSource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> file)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFile()"><!-- --></A><H3>
+getFile</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> <B>getFile</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></B></DD>
+<DD>Get the human readable name for this SequenceSource
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html#getTitle()">getTitle</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="FileSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Identifiable.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Identifiable.html
new file mode 100644
index 0000000..bd197f4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Identifiable.html
@@ -0,0 +1,217 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+Identifiable
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Identifiable";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Identifiable.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Interface Identifiable</H2>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html">ComplexEditableGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.html">ConsensusSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, <A HREF="../../. [...]
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.html">AbstractComplexSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html">AbstractEditableSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.html">AbstractGappedSequence</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html">Abstract [...]
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Identifiable</B></DL>
+
+<P>
+Identifiable.java
+
+
+ Created: Wed Jul 5 16:04:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Identifiable.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html#getIdentifier()">getIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIdentifier()"><!-- --></A><H3>
+getIdentifier</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A> <B>getIdentifier</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Identifiable.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Identifier.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Identifier.html
new file mode 100644
index 0000000..cda9a2b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Identifier.html
@@ -0,0 +1,262 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+Identifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Identifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Identifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Interface Identifier</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html">NoIdentifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Identifier</B></DL>
+
+<P>
+SequenceIdentifier.java
+
+
+ Created: Mon Jul 3 16:07:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Identifier.java,v 1.3 2001/05/24 15:36:13 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#getSource()">getSource</A></B>()</CODE>
+
+<BR>
+ This returns the source of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Gets a human readable title for the Sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSource()"><!-- --></A><H3>
+getSource</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> <B>getSource</B>()</PRE>
+<DL>
+<DD>This returns the source of the sequence. This might be a File
+ object if the sequence has been read straight from file, or a URL
+ from the internet. Alternatively it could be a Java Obect
+ reference if the sequence has been retrieved by calculation, say
+ of a Consensus.
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSource(uk.ac.man.bioinf.sequence.identifier.Source)"><!-- --></A><H3>
+setSource</H3>
+<PRE>
+public void <B>setSource</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD>Gets a human readable title for the Sequence
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Identifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html
new file mode 100644
index 0000000..338e5a1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html
@@ -0,0 +1,242 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+MalformedAccessionException
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="MalformedAccessionException";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MalformedAccessionException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class MalformedAccessionException</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">java.lang.Throwable</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html">java.lang.Exception</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html">java.lang.RuntimeException</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">java.lang.IllegalArgumentException</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>MalformedAccessionException</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html">IllegalArgumentException</A></DL>
+
+<P>
+MalformedAccessionException.java
+
+ Used to indicate an inappropriate accession number has been
+ entered.
+
+ Created: Wed Jul 5 14:17:19 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: MalformedAccessionException.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.sequence.identifier.MalformedAccessionException">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html#MalformedAccessionException(java.lang.String)">MalformedAccessionException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.lang.Throwable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#fillInStackTrace()">fillInStackTrace</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getCause()">getCause</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getLocalizedMessage()">getLocalizedMessage</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html#getMessage()">getMessage</A>, <A HREF="http:// [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="MalformedAccessionException(java.lang.String)"><!-- --></A><H3>
+MalformedAccessionException</H3>
+<PRE>
+public <B>MalformedAccessionException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> message)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="MalformedAccessionException.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.lang.Throwable">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html
new file mode 100644
index 0000000..a095ee0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html
@@ -0,0 +1,328 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+NoIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class NoIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.NoIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoIdentifier</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DL>
+
+<P>
+NoSequenceIdentifier.java
+
+
+ Created: Wed Jul 5 18:42:11 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoIdentifier.java,v 1.3 2001/05/24 15:36:13 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#NoIdentifier()">NoIdentifier</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#NoIdentifier(uk.ac.man.bioinf.sequence.identifier.Source)">NoIdentifier</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#getSource()">getSource</A></B>()</CODE>
+
+<BR>
+ This returns the source of the sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Gets a human readable title for the Sequence</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoIdentifier()"><!-- --></A><H3>
+NoIdentifier</H3>
+<PRE>
+public <B>NoIdentifier</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="NoIdentifier(uk.ac.man.bioinf.sequence.identifier.Source)"><!-- --></A><H3>
+NoIdentifier</H3>
+<PRE>
+public <B>NoIdentifier</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getSource()"><!-- --></A><H3>
+getSource</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> <B>getSource</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></B></DD>
+<DD>This returns the source of the sequence. This might be a File
+ object if the sequence has been read straight from file, or a URL
+ from the internet. Alternatively it could be a Java Obect
+ reference if the sequence has been retrieved by calculation, say
+ of a Consensus.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#getSource()">getSource</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setSource(uk.ac.man.bioinf.sequence.identifier.Source)"><!-- --></A><H3>
+setSource</H3>
+<PRE>
+public void <B>setSource</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></B></DD>
+<DD>Gets a human readable title for the Sequence
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html#getTitle()">getTitle</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/NoSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/NoSource.html
new file mode 100644
index 0000000..6f8f975
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/NoSource.html
@@ -0,0 +1,262 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+NoSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NoSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class NoSource</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.NoSource</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>NoSource</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DL>
+
+<P>
+NoSource.java
+
+
+ Created: Wed Jul 5 18:11:08 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NoSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html#NoSource()">NoSource</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Get the human readable name for this SequenceSource</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NoSource()"><!-- --></A><H3>
+NoSource</H3>
+<PRE>
+public <B>NoSource</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></B></DD>
+<DD>Get the human readable name for this SequenceSource
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html#getTitle()">getTitle</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NoSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/ReaderSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/ReaderSource.html
new file mode 100644
index 0000000..1bfe3a0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/ReaderSource.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+ReaderSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ReaderSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ReaderSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.SimpleSource">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class ReaderSource</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">uk.ac.man.bioinf.sequence.identifier.SimpleSource</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.ReaderSource</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ReaderSource</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">SimpleSource</A></DL>
+
+<P>
+ReaderSource.java
+
+ This class identify the specific reader which was used to load the
+ identifiable object. There is not really a lot which can be done
+ with an object cast as a Reader, so essentially it just uses its
+ toString method at the time that its called.
+
+ Created: Fri Sep 8 18:15:25 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ReaderSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html#ReaderSource(java.io.Reader)">ReaderSource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.SimpleSource"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">SimpleSource</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html#getTitle()">getTitle</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ReaderSource(java.io.Reader)"><!-- --></A><H3>
+ReaderSource</H3>
+<PRE>
+public <B>ReaderSource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ReaderSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.SimpleSource">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SequenceSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SequenceSource.html
new file mode 100644
index 0000000..6911118
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SequenceSource.html
@@ -0,0 +1,221 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+SequenceSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Interface SequenceSource</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>SequenceSource</B></DL>
+
+<P>
+SequenceSource.java
+
+ This class represents the source that is used to produce a
+ sequence. Source means for example, the physical location, or means
+ that were used to retrieve this sequence, such as file name, URL,
+ or the name of the program that was used to retrieve the sequence.
+
+ Created: Tue Jul 4 14:50:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Get the human readable name for this SequenceSource</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD>Get the human readable name for this SequenceSource
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html
new file mode 100644
index 0000000..4c668b6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+SimpleIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SimpleIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SimpleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class SimpleIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SimpleIdentifier</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></DL>
+
+<P>
+SimpleIdentifier.java
+
+
+ Created: Wed Jul 5 19:30:33 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SimpleIdentifier.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html#SimpleIdentifier(java.lang.String)">SimpleIdentifier</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html#SimpleIdentifier(java.lang.String, uk.ac.man.bioinf.sequence.identifier.Source)">SimpleIdentifier</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Gets a human readable title for the Sequence</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#getSource()">getSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SimpleIdentifier(java.lang.String)"><!-- --></A><H3>
+SimpleIdentifier</H3>
+<PRE>
+public <B>SimpleIdentifier</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="SimpleIdentifier(java.lang.String, uk.ac.man.bioinf.sequence.identifier.Source)"><!-- --></A><H3>
+SimpleIdentifier</H3>
+<PRE>
+public <B>SimpleIdentifier</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title,
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></CODE></B></DD>
+<DD>Gets a human readable title for the Sequence
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SimpleIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SimpleSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SimpleSource.html
new file mode 100644
index 0000000..c9d18c1
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SimpleSource.html
@@ -0,0 +1,266 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+SimpleSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SimpleSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SimpleSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class SimpleSource</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.SimpleSource</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html">ReaderSource</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SimpleSource</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></DL>
+
+<P>
+SimpleSource.java
+
+ Utility class mainly meant to extend from.
+
+ Created: Fri Sep 8 18:18:15 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SimpleSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html#SimpleSource(java.lang.String)">SimpleSource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Get the human readable name for this SequenceSource</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SimpleSource(java.lang.String)"><!-- --></A><H3>
+SimpleSource</H3>
+<PRE>
+public <B>SimpleSource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> title)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></B></DD>
+<DD>Get the human readable name for this SequenceSource
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html#getTitle()">getTitle</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SimpleSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Source.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Source.html
new file mode 100644
index 0000000..2736693
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/Source.html
@@ -0,0 +1,221 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:37 BST 2002 -->
+<TITLE>
+Source
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Source";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Source.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Interface Source</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html">FileSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html">NoSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html">SimpleSource</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Source</B></DL>
+
+<P>
+SequenceSource.java
+
+ This class represents the source that is used to produce a
+ sequence. Source means for example, the physical location, or means
+ that were used to retrieve this sequence, such as file name, URL,
+ or the name of the program that was used to retrieve the sequence.
+
+ Created: Tue Jul 4 14:50:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Source.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Get the human readable name for this SequenceSource</TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD>Get the human readable name for this SequenceSource
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Source.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html
new file mode 100644
index 0000000..85e54d5
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html
@@ -0,0 +1,294 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+StreamSequenceSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="StreamSequenceSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="StreamSequenceSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class StreamSequenceSource</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html">URLSequenceSource</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>StreamSequenceSource</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A></DL>
+
+<P>
+StreamSequenceSource.java
+
+
+ Created: Tue Jul 4 17:30:29 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: StreamSequenceSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#StreamSequenceSource(java.io.Reader, java.lang.String)">StreamSequenceSource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> format)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#getFormat()">getFormat</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#getReader()">getReader</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.SequenceSource"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html#getTitle()">getTitle</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="StreamSequenceSource(java.io.Reader, java.lang.String)"><!-- --></A><H3>
+StreamSequenceSource</H3>
+<PRE>
+public <B>StreamSequenceSource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> reader,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> format)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFormat()"><!-- --></A><H3>
+getFormat</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getFormat</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getReader()"><!-- --></A><H3>
+getReader</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Reader.html">Reader</A> <B>getReader</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="StreamSequenceSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html
new file mode 100644
index 0000000..f778c3c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html
@@ -0,0 +1,283 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+SwissProtIdentifier
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SwissProtIdentifier";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SwissProtIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class SwissProtIdentifier</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.SwissProtIdentifier</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SwissProtIdentifier</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A></DL>
+
+<P>
+SwissProtIdentifier.java
+
+
+ Created: Wed Jul 5 14:16:55 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SwissProtIdentifier.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html#SwissProtIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, java.lang.String)">SwissProtIdentifier</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accessionNumber)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html#getDatabaseName()">getDatabaseName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.DatabaseIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getAccession()">getAccession</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getTitle()">getTitle</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html">AbstractIdentifier</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#getSource()">getSource</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html#setSource(uk.ac.man.bioinf.sequence.identifier.Source)">setSource</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SwissProtIdentifier(uk.ac.man.bioinf.sequence.identifier.Source, java.lang.String)"><!-- --></A><H3>
+SwissProtIdentifier</H3>
+<PRE>
+public <B>SwissProtIdentifier</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A> source,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> accessionNumber)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html">MalformedAccessionException</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getDatabaseName()"><!-- --></A><H3>
+getDatabaseName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getDatabaseName</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html#getDatabaseName()">getDatabaseName</A></CODE> in class <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html">DatabaseIdentifier</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SwissProtIdentifier.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html
new file mode 100644
index 0000000..f1ef1dc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+URLSequenceSource
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="URLSequenceSource";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="URLSequenceSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.identifier</FONT>
+<BR>
+Class URLSequenceSource</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.identifier.URLSequenceSource</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>URLSequenceSource</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A></DL>
+
+<P>
+URLSequenceSource.java
+
+ A source for a sequence stored at a URL.
+
+ Created: Tue Jul 4 17:47:31 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: URLSequenceSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html#URLSequenceSource(java.net.URL, java.lang.String)">URLSequenceSource</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> url,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> format)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html#getTitle()">getTitle</A></B>()</CODE>
+
+<BR>
+ Get the human readable name for this SequenceSource</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html#getURL()">getURL</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.identifier.StreamSequenceSource"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html">StreamSequenceSource</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#getFormat()">getFormat</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html#getReader()">getReader</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="URLSequenceSource(java.net.URL, java.lang.String)"><!-- --></A><H3>
+URLSequenceSource</H3>
+<PRE>
+public <B>URLSequenceSource</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> url,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> format)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getURL()"><!-- --></A><H3>
+getURL</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getURL</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTitle()"><!-- --></A><H3>
+getTitle</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTitle</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A></CODE></B></DD>
+<DD>Get the human readable name for this SequenceSource
+<P>
+<DD><DL>
+
+<DT><B>Returns:</B><DD></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="URLSequenceSource.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-frame.html
new file mode 100644
index 0000000..3cc438f
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-frame.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.identifier()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.identifier()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.identifier</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Identifiable.html" TARGET="classFrame"><I>Identifiable</I></A>
+<BR>
+<A HREF="Identifier.html" TARGET="classFrame"><I>Identifier</I></A>
+<BR>
+<A HREF="SequenceSource.html" TARGET="classFrame"><I>SequenceSource</I></A>
+<BR>
+<A HREF="Source.html" TARGET="classFrame"><I>Source</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractIdentifier.html" TARGET="classFrame">AbstractIdentifier</A>
+<BR>
+<A HREF="DatabaseIdentifier.html" TARGET="classFrame">DatabaseIdentifier</A>
+<BR>
+<A HREF="FileSource.html" TARGET="classFrame">FileSource</A>
+<BR>
+<A HREF="NoIdentifier.html" TARGET="classFrame">NoIdentifier</A>
+<BR>
+<A HREF="NoSource.html" TARGET="classFrame">NoSource</A>
+<BR>
+<A HREF="ReaderSource.html" TARGET="classFrame">ReaderSource</A>
+<BR>
+<A HREF="SimpleIdentifier.html" TARGET="classFrame">SimpleIdentifier</A>
+<BR>
+<A HREF="SimpleSource.html" TARGET="classFrame">SimpleSource</A>
+<BR>
+<A HREF="StreamSequenceSource.html" TARGET="classFrame">StreamSequenceSource</A>
+<BR>
+<A HREF="SwissProtIdentifier.html" TARGET="classFrame">SwissProtIdentifier</A>
+<BR>
+<A HREF="URLSequenceSource.html" TARGET="classFrame">URLSequenceSource</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="MalformedAccessionException.html" TARGET="classFrame">MalformedAccessionException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-summary.html
new file mode 100644
index 0000000..3bffec9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-summary.html
@@ -0,0 +1,260 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.identifier()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.identifier()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.identifier
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Identifiable.html"><I>Identifiable</I></A></B></TD>
+<TD>Identifiable.java
+
+
+ Created: Wed Jul 5 16:04:31 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Identifier.html"><I>Identifier</I></A></B></TD>
+<TD>SequenceIdentifier.java
+
+
+ Created: Mon Jul 3 16:07:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceSource.html"><I>SequenceSource</I></A></B></TD>
+<TD>SequenceSource.java
+
+ This class represents the source that is used to produce a
+ sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Source.html"><I>Source</I></A></B></TD>
+<TD>SequenceSource.java
+
+ This class represents the source that is used to produce a
+ sequence.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractIdentifier.html">AbstractIdentifier</A></B></TD>
+<TD>AbstractSequenceIdentifier.java
+
+
+ Created: Wed Jul 5 16:00:43 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DatabaseIdentifier.html">DatabaseIdentifier</A></B></TD>
+<TD>DatabaseIdentifier.java
+
+
+ Created: Wed Jul 5 14:11:46 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="FileSource.html">FileSource</A></B></TD>
+<TD>FileSource.java
+
+
+ Created: Fri Sep 8 18:57:27 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoIdentifier.html">NoIdentifier</A></B></TD>
+<TD>NoSequenceIdentifier.java
+
+
+ Created: Wed Jul 5 18:42:11 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoSource.html">NoSource</A></B></TD>
+<TD>NoSource.java
+
+
+ Created: Wed Jul 5 18:11:08 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ReaderSource.html">ReaderSource</A></B></TD>
+<TD>ReaderSource.java
+
+ This class identify the specific reader which was used to load the
+ identifiable object.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SimpleIdentifier.html">SimpleIdentifier</A></B></TD>
+<TD>SimpleIdentifier.java
+
+
+ Created: Wed Jul 5 19:30:33 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SimpleSource.html">SimpleSource</A></B></TD>
+<TD>SimpleSource.java
+
+ Utility class mainly meant to extend from.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="StreamSequenceSource.html">StreamSequenceSource</A></B></TD>
+<TD>StreamSequenceSource.java
+
+
+ Created: Tue Jul 4 17:30:29 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SwissProtIdentifier.html">SwissProtIdentifier</A></B></TD>
+<TD>SwissProtIdentifier.java
+
+
+ Created: Wed Jul 5 14:16:55 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="URLSequenceSource.html">URLSequenceSource</A></B></TD>
+<TD>URLSequenceSource.java
+
+ A source for a sequence stored at a URL.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MalformedAccessionException.html">MalformedAccessionException</A></B></TD>
+<TD>MalformedAccessionException.java
+
+ Used to indicate an inappropriate accession number has been
+ entered.</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-tree.html
new file mode 100644
index 0000000..29cc30a
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/identifier/package-tree.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.identifier Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.identifier Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.identifier
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.html"><B>AbstractIdentifier</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.html"><B>DatabaseIdentifier</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.html"><B>SwissProtIdentifier</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.html"><B>SimpleIdentifier</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/FileSource.html"><B>FileSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoIdentifier.html"><B>NoIdentifier</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html">Identifier</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/NoSource.html"><B>NoSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SimpleSource.html"><B>SimpleSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Source.html">Source</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/ReaderSource.html"><B>ReaderSource</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.html"><B>StreamSequenceSource</B></A> (implements uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html">SequenceSource</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.html"><B>URLSequenceSource</B></A></UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/IllegalArgumentException.html"><B>IllegalArgumentException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.html"><B>MalformedAccessionException</B></A></UL>
+</UL>
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/Identifier.html"><B>Identifier</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/SequenceSource.html"><B>S [...]
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/group/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/package-frame.html
new file mode 100644
index 0000000..e50f6c2
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/package-frame.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../uk/ac/man/bioinf/sequence/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ComplexEditableGappedSequence.html" TARGET="classFrame"><I>ComplexEditableGappedSequence</I></A>
+<BR>
+<A HREF="EditableSequence.html" TARGET="classFrame"><I>EditableSequence</I></A>
+<BR>
+<A HREF="Element.html" TARGET="classFrame"><I>Element</I></A>
+<BR>
+<A HREF="MutableSequence.html" TARGET="classFrame"><I>MutableSequence</I></A>
+<BR>
+<A HREF="Residue.html" TARGET="classFrame"><I>Residue</I></A>
+<BR>
+<A HREF="Sequence.html" TARGET="classFrame"><I>Sequence</I></A>
+<BR>
+<A HREF="SequenceType.html" TARGET="classFrame"><I>SequenceType</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractEditableSequence.html" TARGET="classFrame">AbstractEditableSequence</A>
+<BR>
+<A HREF="AbstractMutableSequence.html" TARGET="classFrame">AbstractMutableSequence</A>
+<BR>
+<A HREF="AbstractSequence.html" TARGET="classFrame">AbstractSequence</A>
+<BR>
+<A HREF="DefaultEditableSequence.html" TARGET="classFrame">DefaultEditableSequence</A>
+<BR>
+<A HREF="DefaultSequence.html" TARGET="classFrame">DefaultSequence</A>
+<BR>
+<A HREF="EmptySequence.html" TARGET="classFrame">EmptySequence</A>
+<BR>
+<A HREF="SequenceFactory.html" TARGET="classFrame">SequenceFactory</A>
+<BR>
+<A HREF="Sequences.html" TARGET="classFrame">Sequences</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Exceptions</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="InvalidSequenceTypeException.html" TARGET="classFrame">InvalidSequenceTypeException</A>
+<BR>
+<A HREF="NoSuchSequenceElementException.html" TARGET="classFrame">NoSuchSequenceElementException</A>
+<BR>
+<A HREF="SequenceException.html" TARGET="classFrame">SequenceException</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/package-summary.html
new file mode 100644
index 0000000..8ad68b0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/package-summary.html
@@ -0,0 +1,288 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence
+</H2>
+Provides classes for representing mutable sequences.
+<P>
+<B>See:</B>
+<BR>
+ <A HREF="#package_description"><B>Description</B></A>
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexEditableGappedSequence.html"><I>ComplexEditableGappedSequence</I></A></B></TD>
+<TD>ComplexEditableGappedSequence.java
+
+
+ Created: Wed Dec 6 20:08:32 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="EditableSequence.html"><I>EditableSequence</I></A></B></TD>
+<TD>EditableSequence.java
+
+
+ Created: Wed Mar 1 19:39:40 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Element.html"><I>Element</I></A></B></TD>
+<TD>Element.java
+
+ This interface defines an element within a sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MutableSequence.html"><I>MutableSequence</I></A></B></TD>
+<TD>MutableSequence.java
+
+ A marker class to present a sequence which can be changed without
+ the necessity for generating a new sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Residue.html"><I>Residue</I></A></B></TD>
+<TD>Residue.java
+
+ An interface to represent entirely biological elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Sequence.html"><I>Sequence</I></A></B></TD>
+<TD>Sequence.java
+
+ This interface is designed to model a biological sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceType.html"><I>SequenceType</I></A></B></TD>
+<TD>SequenceType.java
+
+ An interface to represent the type of a sequence (e.g: Protein, DNA).</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractEditableSequence.html">AbstractEditableSequence</A></B></TD>
+<TD>AbstractEditableSequence.java
+
+ This class provides trivial implementations of all of those methods
+ which can be defined in terms of the others of the EditableSequence
+ interface, and also ensures that the event handling occurs correctly
+
+ Created: Fri Mar 3 12:11:49 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractMutableSequence.html">AbstractMutableSequence</A></B></TD>
+<TD>AbstractMutableSequence.java
+
+
+ Created: Thu Mar 2 20:20:02 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequence.html">AbstractSequence</A></B></TD>
+<TD>AbstractSequence.java
+
+ Provides some of the methods for sequence.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultEditableSequence.html">DefaultEditableSequence</A></B></TD>
+<TD>DefaultEditableSequence.java
+
+
+ Created: Thu Mar 2 20:27:46 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DefaultSequence.html">DefaultSequence</A></B></TD>
+<TD>DefaultSequence.java
+
+
+ Created: Thu Mar 2 15:32:25 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="EmptySequence.html">EmptySequence</A></B></TD>
+<TD>EmptySequence.java
+
+
+ Created: Mon Feb 5 17:53:37 2001</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceFactory.html">SequenceFactory</A></B></TD>
+<TD>SequenceFactory provides a simple way into the Sequence API.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Sequences.html">Sequences</A></B></TD>
+<TD>Sequences.java
+
+
+ Created: Tue Mar 14 13:43:59 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Exception Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="InvalidSequenceTypeException.html">InvalidSequenceTypeException</A></B></TD>
+<TD>InvalidSequenceTypeException.java
+
+ Exception to signal that an attempt has been made to use a sequence
+ of an invalid type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NoSuchSequenceElementException.html">NoSuchSequenceElementException</A></B></TD>
+<TD>NoSuchSequenceElementException.java
+
+
+ Created: Fri Mar 3 12:22:15 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceException.html">SequenceException</A></B></TD>
+<TD>SequenceException.java
+
+
+ Created: Thu Mar 2 17:07:48 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<A NAME="package_description"><!-- --></A><H2>
+Package uk.ac.man.bioinf.sequence Description
+</H2>
+
+<P>
+Provides classes for representing mutable sequences.
+ As well as providing interfaces which represent the notion of a
+ sequence, a full event model is provided.
+<P>
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/package-tree.html
new file mode 100644
index 0000000..aeba509
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/package-tree.html
@@ -0,0 +1,187 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:12 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractSequence.html"><B>AbstractSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractMutableSequence.html"><B>AbstractMutableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html">MutableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/AbstractEditableSequence.html"><B>AbstractEditableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultEditableSequence.html"><B>DefaultEditableSequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>)
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/DefaultSequence.html"><B>DefaultSequence</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EmptySequence.html"><B>EmptySequence</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceFactory.html"><B>SequenceFactory</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequences.html"><B>Sequences</B></A><LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html"><B>Throwable</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/a [...]
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Exception.html"><B>Exception</B></A><UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/RuntimeException.html"><B>RuntimeException</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.html"><B>InvalidSequenceTypeException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.html"><B>NoSuchSequenceElementException</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceException.html"><B>SequenceExcep [...]
+</UL>
+</UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>Element</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Residue.html"><B>Residue</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.identifier.<A HREF="../../../../../uk/ac/man/bioinf/sequence/identifier/Identifiable.html"><B>Identifiable</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html"><B>Sequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HR [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html"><B>ComplexSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../. [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html">SequenceEventProvider</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HR [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html"><B>EditableSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, uk.ac.man.bioinf.sequence [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../ [...]
+</UL>
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEventProvider.html"><B>SequenceEventProvider</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/MutableSequence.html"><B>MutableSequence</B></A> (also extends uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A>)
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HR [...]
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html"><B>EditableSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A>, uk.ac.man.bioinf.sequence [...]
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.alignment.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html"><B>GappedSequence</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.html"><B>ComplexEditableGappedSequence</B></A> (also extends uk.ac.man.bioinf.sequence.complex.<A HREF="../../../../../uk/ac/man/bioinf/sequence/complex/ComplexSequence.html">ComplexSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/EditableSequence.html">EditableSequence</A>, uk.ac.man.bioinf.sequence.<A HREF="../../ [...]
+</UL>
+</UL>
+</UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../uk/ac/man/bioinf/sequence/SequenceType.html"><B>SequenceType</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/module/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html
new file mode 100644
index 0000000..f4e659e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+ComplexElementAndModificationTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexElementAndModificationTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElementAndModificationTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class ComplexElementAndModificationTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.ComplexElementAndModificationTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ComplexElementAndModificationTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ComplexElementAndModificationTest.java
+
+
+ Created: Tue Feb 29 11:32:15 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexElementAndModificationTest.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html#ComplexElementAndModificationTest()">ComplexElementAndModificationTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ComplexElementAndModificationTest()"><!-- --></A><H3>
+ComplexElementAndModificationTest</H3>
+<PRE>
+public <B>ComplexElementAndModificationTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexElementAndModificationTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html
new file mode 100644
index 0000000..491d12e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+ComplexSequenceTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ComplexSequenceTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class ComplexSequenceTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.ComplexSequenceTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ComplexSequenceTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ComplexSequenceTest.java
+
+
+ Created: Mon Nov 27 14:09:29 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ComplexSequenceTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html#ComplexSequenceTest()">ComplexSequenceTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html#createRNAResidues()">createRNAResidues</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ComplexSequenceTest()"><!-- --></A><H3>
+ComplexSequenceTest</H3>
+<PRE>
+public <B>ComplexSequenceTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="createRNAResidues()"><!-- --></A><H3>
+createRNAResidues</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>[] <B>createRNAResidues</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ComplexSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html
new file mode 100644
index 0000000..f51d34c
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html
@@ -0,0 +1,271 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+EditableSequenceTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="EditableSequenceTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EditableSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class EditableSequenceTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.EditableSequenceTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>EditableSequenceTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+EditableSequenceTest.java
+
+
+ Created: Fri Mar 3 16:08:35 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: EditableSequenceTest.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html#EditableSequenceTest()">EditableSequenceTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html#printSeq(uk.ac.man.bioinf.sequence.Sequence)">printSeq</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="EditableSequenceTest()"><!-- --></A><H3>
+EditableSequenceTest</H3>
+<PRE>
+public <B>EditableSequenceTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printSeq(uk.ac.man.bioinf.sequence.Sequence)"><!-- --></A><H3>
+printSeq</H3>
+<PRE>
+public static void <B>printSeq</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Sequence.html">Sequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EditableSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html
new file mode 100644
index 0000000..de04452
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html
@@ -0,0 +1,271 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+GappableSequenceTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappableSequenceTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappableSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class GappableSequenceTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.GappableSequenceTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>GappableSequenceTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+GappableSequenceTest.java
+
+
+ Created: Tue Mar 7 13:45:10 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappableSequenceTest.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html#GappableSequenceTest()">GappableSequenceTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html#printSeq(uk.ac.man.bioinf.sequence.alignment.GappedSequence)">printSeq</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GappableSequenceTest()"><!-- --></A><H3>
+GappableSequenceTest</H3>
+<PRE>
+public <B>GappableSequenceTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="printSeq(uk.ac.man.bioinf.sequence.alignment.GappedSequence)"><!-- --></A><H3>
+printSeq</H3>
+<PRE>
+public static void <B>printSeq</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/GappedSequence.html">GappedSequence</A> seq)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappableSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html
new file mode 100644
index 0000000..d174a62
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html
@@ -0,0 +1,254 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+GappedSequenceTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="GappedSequenceTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class GappedSequenceTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.GappedSequenceTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>GappedSequenceTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+GappedSequenceTest.java
+
+
+ Created: Wed Jun 7 16:18:11 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: GappedSequenceTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html#GappedSequenceTest()">GappedSequenceTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GappedSequenceTest()"><!-- --></A><H3>
+GappedSequenceTest</H3>
+<PRE>
+public <B>GappedSequenceTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappableSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="GappedSequenceTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html
new file mode 100644
index 0000000..d07da67
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html
@@ -0,0 +1,338 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+SequenceAlignmentTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignmentTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class SequenceAlignmentTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.SequenceAlignmentTest</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListene [...]
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceAlignmentTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListen [...]
+
+<P>
+SequenceAlignmentTest.java
+
+
+ Created: Fri Mar 10 12:39:40 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignmentTest.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)</CODE>
+
+<BR>
+ Method called before a change occurs to an alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)</CODE>
+
+<BR>
+ Method signalled before a prospective change occurs</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.html">VetoableSequenceEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></B></DD>
+<DD>Method signalled before a prospective change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent)">vetoableChangeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.html">VetoableSequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/event/SequenceVetoException.html">SequenceVetoException</A></CODE> - if the listener does not wish
+ the event to occur.</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)"><!-- --></A><H3>
+vetoableChangeOccurred</H3>
+<PRE>
+public void <B>vetoableChangeOccurred</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.html">VetoableAlignmentEvent</A> event)
+ throws <A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A></CODE></B></DD>
+<DD>Method called before a change occurs to an alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html#vetoableChangeOccurred(uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent)">vetoableChangeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.html">VetoableAlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> -
+<DT><B>Throws:</B>
+<DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.html">AlignmentVetoException</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/GappedSequenceTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html
new file mode 100644
index 0000000..8bbe967
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html
@@ -0,0 +1,254 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+SequenceColumnTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceColumnTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceColumnTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class SequenceColumnTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.SequenceColumnTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceColumnTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceColumnTest.java
+
+
+ Created: Wed Jun 7 15:41:17 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceColumnTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html#SequenceColumnTest()">SequenceColumnTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceColumnTest()"><!-- --></A><H3>
+SequenceColumnTest</H3>
+<PRE>
+public <B>SequenceColumnTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A></CODE></DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceColumnTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html
new file mode 100644
index 0000000..f2d41b3
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+SequenceFactoryTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceFactoryTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequencesTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceFactoryTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class SequenceFactoryTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.SequenceFactoryTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequenceFactoryTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequenceFactoryTest.java
+
+
+ Created: Tue Nov 14 18:21:42 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceFactoryTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html#SequenceFactoryTest()">SequenceFactoryTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceFactoryTest()"><!-- --></A><H3>
+SequenceFactoryTest</H3>
+<PRE>
+public <B>SequenceFactoryTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequencesTest.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceFactoryTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequencesTest.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequencesTest.html
new file mode 100644
index 0000000..b58a70d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/SequencesTest.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+SequencesTest
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequencesTest";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequencesTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.test</FONT>
+<BR>
+Class SequencesTest</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.test.SequencesTest</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>SequencesTest</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+SequencesTest.java
+
+
+ Created: Tue Mar 14 14:19:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequencesTest.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequencesTest.html#SequencesTest()">SequencesTest</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequencesTest.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequencesTest()"><!-- --></A><H3>
+SequencesTest</H3>
+<PRE>
+public <B>SequencesTest</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequencesTest.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-frame.html
new file mode 100644
index 0000000..e99f2f9
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-frame.html
@@ -0,0 +1,48 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.test</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="ComplexElementAndModificationTest.html" TARGET="classFrame">ComplexElementAndModificationTest</A>
+<BR>
+<A HREF="ComplexSequenceTest.html" TARGET="classFrame">ComplexSequenceTest</A>
+<BR>
+<A HREF="EditableSequenceTest.html" TARGET="classFrame">EditableSequenceTest</A>
+<BR>
+<A HREF="GappableSequenceTest.html" TARGET="classFrame">GappableSequenceTest</A>
+<BR>
+<A HREF="GappedSequenceTest.html" TARGET="classFrame">GappedSequenceTest</A>
+<BR>
+<A HREF="SequenceAlignmentTest.html" TARGET="classFrame">SequenceAlignmentTest</A>
+<BR>
+<A HREF="SequenceColumnTest.html" TARGET="classFrame">SequenceColumnTest</A>
+<BR>
+<A HREF="SequenceFactoryTest.html" TARGET="classFrame">SequenceFactoryTest</A>
+<BR>
+<A HREF="SequencesTest.html" TARGET="classFrame">SequencesTest</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-summary.html
new file mode 100644
index 0000000..00b64a6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-summary.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.test()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.test()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.test
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexElementAndModificationTest.html">ComplexElementAndModificationTest</A></B></TD>
+<TD>ComplexElementAndModificationTest.java
+
+
+ Created: Tue Feb 29 11:32:15 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ComplexSequenceTest.html">ComplexSequenceTest</A></B></TD>
+<TD>ComplexSequenceTest.java
+
+
+ Created: Mon Nov 27 14:09:29 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="EditableSequenceTest.html">EditableSequenceTest</A></B></TD>
+<TD>EditableSequenceTest.java
+
+
+ Created: Fri Mar 3 16:08:35 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappableSequenceTest.html">GappableSequenceTest</A></B></TD>
+<TD>GappableSequenceTest.java
+
+
+ Created: Tue Mar 7 13:45:10 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="GappedSequenceTest.html">GappedSequenceTest</A></B></TD>
+<TD>GappedSequenceTest.java
+
+
+ Created: Wed Jun 7 16:18:11 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignmentTest.html">SequenceAlignmentTest</A></B></TD>
+<TD>SequenceAlignmentTest.java
+
+
+ Created: Fri Mar 10 12:39:40 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceColumnTest.html">SequenceColumnTest</A></B></TD>
+<TD>SequenceColumnTest.java
+
+
+ Created: Wed Jun 7 15:41:17 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceFactoryTest.html">SequenceFactoryTest</A></B></TD>
+<TD>SequenceFactoryTest.java
+
+
+ Created: Tue Nov 14 18:21:42 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequencesTest.html">SequencesTest</A></B></TD>
+<TD>SequencesTest.java
+
+
+ Created: Tue Mar 14 14:19:44 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-tree.html
new file mode 100644
index 0000000..52745f8
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/test/package-tree.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.test Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.test Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.test
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.html"><B>ComplexElementAndModificationTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.html"><B>ComplexSequenceTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/EditableSeque [...]
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceColumnTest.html"><B>SequenceColumnTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.html"><B>SequenceFactoryTest</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.test.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/SequencesTest.html"><B>SequencesTest</B></A></UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/identifier/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractElement.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractElement.html
new file mode 100644
index 0000000..9357c9b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractElement.html
@@ -0,0 +1,323 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+AbstractElement
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractElement";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractElement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class AbstractElement</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.AbstractElement</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractElement</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></DL>
+
+<P>
+AbstractElement.java
+
+
+ Created: Mon Feb 28 16:10:45 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractElement.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#AbstractElement(java.lang.String, char)">AbstractElement</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString,
+ char toChar)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#getAllSequenceElements(java.lang.Class)">getAllSequenceElements</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</CODE>
+
+<BR>
+ Returns all the elements.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> char</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#toChar()">toChar</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractElement(java.lang.String, char)"><!-- --></A><H3>
+AbstractElement</H3>
+<PRE>
+public <B>AbstractElement</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString,
+ char toChar)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="toChar()"><!-- --></A><H3>
+toChar</H3>
+<PRE>
+public char <B>toChar</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAllSequenceElements(java.lang.Class)"><!-- --></A><H3>
+getAllSequenceElements</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getAllSequenceElements</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</PRE>
+<DL>
+<DD>Returns all the elements. This method basically switches the type
+ of the
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>cla</CODE> - the class of the elements
+<DT><B>Returns:</B><DD>the Elements of the class</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractElement.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html
new file mode 100644
index 0000000..295e8ca
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html
@@ -0,0 +1,335 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+AbstractEnumeratedSequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractEnumeratedSequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeratedSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class AbstractEnumeratedSequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractSequenceType</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>AbstractEnumeratedSequenceType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></DL>
+
+<P>
+AbstractEnumeratedSequenceType.java
+
+
+ Created: Tue Jun 13 13:20:11 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractEnumeratedSequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements">elements</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#AbstractEnumeratedSequenceType(uk.ac.man.bioinf.sequence.Element[][], java.lang.String)">AbstractEnumeratedSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[][] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#AbstractEnumeratedSequenceType(uk.ac.man.bioinf.sequence.Element[], java.lang.String)">AbstractEnumeratedSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getElementForInt(int)">getElementForInt</A></B>(int index)</CODE>
+
+<BR>
+ The inverse of the method getIntForElement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ This method is present as a performance enhancement.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()">getName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)">isElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])">isElement</A>, <A HREF="../../../.. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractEnumeratedSequenceType(uk.ac.man.bioinf.sequence.Element[], java.lang.String)"><!-- --></A><H3>
+AbstractEnumeratedSequenceType</H3>
+<PRE>
+public <B>AbstractEnumeratedSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AbstractEnumeratedSequenceType(uk.ac.man.bioinf.sequence.Element[][], java.lang.String)"><!-- --></A><H3>
+AbstractEnumeratedSequenceType</H3>
+<PRE>
+public <B>AbstractEnumeratedSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[][] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getIntForElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+getIntForElement</H3>
+<PRE>
+public int <B>getIntForElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>This method is present as a performance enhancement. For every
+ Element this method should return a unique and repeatable int,
+ starting at 0 and ending at size() - 1 for all possible
+ Elements. This enables the Element to be used as an index for an
+ array which in turn allows implementation of efficient look up
+ tables, rather than using a hashtable.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>a int</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementForInt(int)"><!-- --></A><H3>
+getElementForInt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementForInt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>The inverse of the method getIntForElement.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - a value of type 'int'
+<DT><B>Returns:</B><DD>a value of type 'Element'</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeratedSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html
new file mode 100644
index 0000000..d2b2886
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html
@@ -0,0 +1,490 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+AbstractSequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractSequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class AbstractSequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.AbstractSequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.html">AbstractComplexSequenceType</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractSequenceType</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DL>
+
+<P>
+AbstractSequenceType.java
+
+
+ Created: Thu Feb 17 13:02:28 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractSequenceType.java,v 1.5 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements">elements</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#AbstractSequenceType(uk.ac.man.bioinf.sequence.Element[][], java.lang.String)">AbstractSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[][] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#AbstractSequenceType(uk.ac.man.bioinf.sequence.Element[], java.lang.String)">AbstractSequenceType</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()">getElements</A></B>()</CODE>
+
+<BR>
+ Returns all the elements available in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the human readable form of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)">isElement</A></B>(char element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])">isElement</A></B>(char[] element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#size()">size</A></B>()</CODE>
+
+<BR>
+ Returns the number of elements in this sequence type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.SequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)">getElementForInt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="elements"><!-- --></A><H3>
+elements</H3>
+<PRE>
+protected <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>elements</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractSequenceType(uk.ac.man.bioinf.sequence.Element[], java.lang.String)"><!-- --></A><H3>
+AbstractSequenceType</H3>
+<PRE>
+public <B>AbstractSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="AbstractSequenceType(uk.ac.man.bioinf.sequence.Element[][], java.lang.String)"><!-- --></A><H3>
+AbstractSequenceType</H3>
+<PRE>
+public <B>AbstractSequenceType</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[][] elements,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> name)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char)">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char[] element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char[])">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns the human readable form of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElements()"><!-- --></A><H3>
+getElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns all the elements available in this sequence type.
+ This array should be freely modifiable, and changes should not
+ percolate backwards iunto the internal data of the sequence
+ type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElements()">getElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns the number of elements in this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#size()">size</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of elements</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/AminoAcid.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AminoAcid.html
new file mode 100644
index 0000000..be63ac0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/AminoAcid.html
@@ -0,0 +1,760 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+AminoAcid
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AminoAcid";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AminoAcid.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class AminoAcid</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">uk.ac.man.bioinf.sequence.types.AbstractElement</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.AminoAcid</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public final class <B>AminoAcid</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A></DL>
+
+<P>
+AminoAcid.java
+
+ A class for the representation of an amino-acid. This class is an
+ enumeration of types.
+
+ Created: Wed Feb 16 20:30:57 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AminoAcid.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ALANINE">ALANINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ANY">ANY</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ARGININE">ARGININE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ASNORASP">ASNORASP</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ASPARAGINE">ASPARAGINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ASPARTICACID">ASPARTICACID</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#CYSTEINE">CYSTEINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLUORGLN">GLUORGLN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLUTAMICACID">GLUTAMICACID</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLUTAMINE">GLUTAMINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#GLYCINE">GLYCINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#HISTIDINE">HISTIDINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#ISOLEUCINE">ISOLEUCINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#LEUCINE">LEUCINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#LYSINE">LYSINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#METHIONINE">METHIONINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#PHENYLALANINE">PHENYLALANINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#PROLINE">PROLINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#SERINE">SERINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#THREONINE">THREONINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#TRYPTOPHAN">TRYPTOPHAN</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#TYROSINE">TYROSINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#VALINE">VALINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#getAll()">getAll</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#getFullName()">getFullName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html#getThreeLetter()">getThreeLetter</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractElement"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#getAllSequenceElements(java.lang.Class)">getAllSequenceElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="GLYCINE"><!-- --></A><H3>
+GLYCINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>GLYCINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ALANINE"><!-- --></A><H3>
+ALANINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ALANINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="VALINE"><!-- --></A><H3>
+VALINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>VALINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="LEUCINE"><!-- --></A><H3>
+LEUCINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>LEUCINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ISOLEUCINE"><!-- --></A><H3>
+ISOLEUCINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ISOLEUCINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="SERINE"><!-- --></A><H3>
+SERINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>SERINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CYSTEINE"><!-- --></A><H3>
+CYSTEINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>CYSTEINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="THREONINE"><!-- --></A><H3>
+THREONINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>THREONINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="METHIONINE"><!-- --></A><H3>
+METHIONINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>METHIONINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="PHENYLALANINE"><!-- --></A><H3>
+PHENYLALANINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>PHENYLALANINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="TYROSINE"><!-- --></A><H3>
+TYROSINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>TYROSINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="TRYPTOPHAN"><!-- --></A><H3>
+TRYPTOPHAN</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>TRYPTOPHAN</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="PROLINE"><!-- --></A><H3>
+PROLINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>PROLINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="HISTIDINE"><!-- --></A><H3>
+HISTIDINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>HISTIDINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="LYSINE"><!-- --></A><H3>
+LYSINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>LYSINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ARGININE"><!-- --></A><H3>
+ARGININE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ARGININE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ASPARTICACID"><!-- --></A><H3>
+ASPARTICACID</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ASPARTICACID</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GLUTAMICACID"><!-- --></A><H3>
+GLUTAMICACID</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>GLUTAMICACID</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ASPARAGINE"><!-- --></A><H3>
+ASPARAGINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ASPARAGINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GLUTAMINE"><!-- --></A><H3>
+GLUTAMINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>GLUTAMINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ASNORASP"><!-- --></A><H3>
+ASNORASP</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ASNORASP</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GLUORGLN"><!-- --></A><H3>
+GLUORGLN</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>GLUORGLN</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="ANY"><!-- --></A><H3>
+ANY</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A> <B>ANY</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getThreeLetter()"><!-- --></A><H3>
+getThreeLetter</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getThreeLetter</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFullName()"><!-- --></A><H3>
+getFullName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getFullName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAll()"><!-- --></A><H3>
+getAll</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A>[] <B>getAll</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AminoAcid.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNANucleotide.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNANucleotide.html
new file mode 100644
index 0000000..0f59266
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNANucleotide.html
@@ -0,0 +1,394 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+DNANucleotide
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DNANucleotide";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DNANucleotide.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class DNANucleotide</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">uk.ac.man.bioinf.sequence.types.AbstractElement</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.DNANucleotide</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DNANucleotide</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A></DL>
+
+<P>
+DNANucleotide.java
+
+
+ Created: Sun Sep 24 17:44:04 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DNANucleotide.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html#ADENOSINE">ADENOSINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html#CYTOSINE">CYTOSINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html#GUANINE">GUANINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html#THIAMINE">THIAMINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html#getAll()">getAll</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html#getFullName()">getFullName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractElement"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#getAllSequenceElements(java.lang.Class)">getAllSequenceElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ADENOSINE"><!-- --></A><H3>
+ADENOSINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A> <B>ADENOSINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GUANINE"><!-- --></A><H3>
+GUANINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A> <B>GUANINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CYTOSINE"><!-- --></A><H3>
+CYTOSINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A> <B>CYTOSINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="THIAMINE"><!-- --></A><H3>
+THIAMINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A> <B>THIAMINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFullName()"><!-- --></A><H3>
+getFullName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getFullName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAll()"><!-- --></A><H3>
+getAll</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>[] <B>getAll</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DNANucleotide.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNAResidue.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNAResidue.html
new file mode 100644
index 0000000..eab8805
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNAResidue.html
@@ -0,0 +1,195 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+DNAResidue
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DNAResidue";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DNAResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Interface DNAResidue</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>DNAResidue</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A></DL>
+
+<P>
+DNAResidue.java
+
+ An interface to represent a DNA residue.
+
+ Created: Mon Feb 28 13:02:09 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DNAResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DNAResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNASequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNASequenceType.html
new file mode 100644
index 0000000..53d1353
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/DNASequenceType.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+DNASequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="DNASequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DNASequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class DNASequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractSequenceType</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.DNASequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>DNASequenceType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></DL>
+
+<P>
+DNASequenceType.java
+
+ This class represents the DNA sequence type, allowing only a set
+ of particular bases.
+
+ Created: Tue Aug 22 18:41:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: DNASequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Julian Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html#instance">instance</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements">elements</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getElementForInt(int)">getElementForInt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()">getName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)">isElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])">isElement</A>, <A HREF="../../../.. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="instance"><!-- --></A><H3>
+instance</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A> <B>instance</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html">DNASequenceType</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="DNASequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/EmptySequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/EmptySequenceType.html
new file mode 100644
index 0000000..56ac538
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/EmptySequenceType.html
@@ -0,0 +1,512 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+EmptySequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="EmptySequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptySequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class EmptySequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.EmptySequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>EmptySequenceType</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DL>
+
+<P>
+EmptySequenceType.java
+
+
+ Created: Tue Aug 1 17:22:00 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: EmptySequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#INSTANCE">INSTANCE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getElementForInt(int)">getElementForInt</A></B>(int index)</CODE>
+
+<BR>
+ The inverse of the method getIntForElement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getElements()">getElements</A></B>()</CODE>
+
+<BR>
+ Returns all the elements available in this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ This method is present as a performance enhancement.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#getName()">getName</A></B>()</CODE>
+
+<BR>
+ Returns the human readable form of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(char)">isElement</A></B>(char element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(char[])">isElement</A></B>(char[] elements)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified element is part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</CODE>
+
+<BR>
+ Returns a boolean as to whether the specified elements are part
+ of this sequence type.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html#size()">size</A></B>()</CODE>
+
+<BR>
+ Returns the number of elements in this sequence type.</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="INSTANCE"><!-- --></A><H3>
+INSTANCE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html">EmptySequenceType</A> <B>INSTANCE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns the number of elements in this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#size()">size</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the number of elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getIntForElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+getIntForElement</H3>
+<PRE>
+public int <B>getIntForElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>This method is present as a performance enhancement. For every
+ Element this method should return a unique and repeatable int,
+ starting at 0 and ending at size() - 1 for all possible
+ Elements. This enables the Element to be used as an index for an
+ array which in turn allows implementation of efficient look up
+ tables, rather than using a hashtable.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>a int</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElementForInt(int)"><!-- --></A><H3>
+getElementForInt</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> <B>getElementForInt</B>(int index)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>The inverse of the method getIntForElement.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElementForInt(int)">getElementForInt</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>index</CODE> - a value of type 'int'
+<DT><B>Returns:</B><DD>a value of type 'Element'</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getElements()"><!-- --></A><H3>
+getElements</H3>
+<PRE>
+public <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] <B>getElements</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns all the elements available in this sequence type.
+ This array should be freely modifiable, and changes should not
+ percolate backwards iunto the internal data of the sequence
+ type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getElements()">getElements</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getName()"><!-- --></A><H3>
+getName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getName</B>()</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns the human readable form of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+
+<DT><B>Returns:</B><DD>the name</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char)">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element)"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A> element)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified element is part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element)">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>element</CODE> - the element
+<DT><B>Returns:</B><DD>whether an element</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(char[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(char[] elements)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(char[])">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isElement(uk.ac.man.bioinf.sequence.Element[])"><!-- --></A><H3>
+isElement</H3>
+<PRE>
+public boolean <B>isElement</B>(<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>[] elements)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></B></DD>
+<DD>Returns a boolean as to whether the specified elements are part
+ of this sequence type.
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html#isElement(uk.ac.man.bioinf.sequence.Element[])">isElement</A></CODE> in interface <CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>elements</CODE> - the elements
+<DT><B>Returns:</B><DD>whether elements</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="EmptySequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/NucleotideResidue.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/NucleotideResidue.html
new file mode 100644
index 0000000..8e7a3e0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/NucleotideResidue.html
@@ -0,0 +1,198 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:32 BST 2002 -->
+<TITLE>
+NucleotideResidue
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="NucleotideResidue";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NucleotideResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Interface NucleotideResidue</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Subinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html">DNANucleotide</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>NucleotideResidue</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DL>
+
+<P>
+NucleotideResidue.java
+
+ An interface to mark up nucleotide residues.
+
+ Created: Mon Feb 28 12:59:40 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: NucleotideResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="NucleotideResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/ProteinResidue.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/ProteinResidue.html
new file mode 100644
index 0000000..a551288
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/ProteinResidue.html
@@ -0,0 +1,195 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+ProteinResidue
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ProteinResidue";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ProteinResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Interface ProteinResidue</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html">AminoAcid</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>ProteinResidue</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DL>
+
+<P>
+ProteinResidue.java
+
+ An interface to represent a protein residue.
+
+ Created: Mon Feb 28 13:08:13 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ProteinResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>J Selley</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ProteinResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html
new file mode 100644
index 0000000..e9ae98e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html
@@ -0,0 +1,290 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+ProteinSequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ProteinSequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ProteinSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class ProteinSequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractSequenceType</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.ProteinSequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ProteinSequenceType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></DL>
+
+<P>
+ProteinSequenceType.java
+
+
+ Created: Fri Mar 3 16:12:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ProteinSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html#instance">instance</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements">elements</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getElementForInt(int)">getElementForInt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()">getName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)">isElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])">isElement</A>, <A HREF="../../../.. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="instance"><!-- --></A><H3>
+instance</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A> <B>instance</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html">ProteinSequenceType</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ProteinSequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNANucleotide.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNANucleotide.html
new file mode 100644
index 0000000..8984d68
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNANucleotide.html
@@ -0,0 +1,396 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+RNANucleotide
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="RNANucleotide";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="RNANucleotide.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class RNANucleotide</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">uk.ac.man.bioinf.sequence.types.AbstractElement</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.RNANucleotide</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public final class <B>RNANucleotide</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A><DT>implements <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A></DL>
+
+<P>
+RNANucleotide.java
+
+ A class for the representation of RNA Nucleotides. This class
+ is an enumeration of types.
+
+ Created: Mon Feb 28 15:42:47 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: RNANucleotide.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Daniel Jameson</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html#ADENOSINE">ADENOSINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html#CYTOSINE">CYTOSINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html#GUANINE">GUANINE</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html#URACIL">URACIL</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html#getAll()">getAll</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html#getFullName()">getFullName</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractElement"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#getAllSequenceElements(java.lang.Class)">getAllSequenceElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ADENOSINE"><!-- --></A><H3>
+ADENOSINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A> <B>ADENOSINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="GUANINE"><!-- --></A><H3>
+GUANINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A> <B>GUANINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="CYTOSINE"><!-- --></A><H3>
+CYTOSINE</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A> <B>CYTOSINE</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="URACIL"><!-- --></A><H3>
+URACIL</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A> <B>URACIL</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getFullName()"><!-- --></A><H3>
+getFullName</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getFullName</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAll()"><!-- --></A><H3>
+getAll</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A>[] <B>getAll</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="RNANucleotide.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNAResidue.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNAResidue.html
new file mode 100644
index 0000000..16dc445
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNAResidue.html
@@ -0,0 +1,195 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:33 BST 2002 -->
+<TITLE>
+RNAResidue
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="RNAResidue";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="RNAResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Interface RNAResidue</H2>
+<DL>
+<DT><B>All Superinterfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html">Residue</A></DD>
+</DL>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html">RNANucleotide</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>RNAResidue</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html">NucleotideResidue</A></DL>
+
+<P>
+RNAResidue.java
+
+ An interface to represent an RNA Residue
+
+ Created: Mon Feb 28 13:02:16 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: RNAResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Daniel Jameson</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.Element"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html">Element</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html#toChar()">toChar</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="RNAResidue.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | METHOD</FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNASequenceType.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNASequenceType.html
new file mode 100644
index 0000000..2ee8fc7
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/RNASequenceType.html
@@ -0,0 +1,317 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:34 BST 2002 -->
+<TITLE>
+RNASequenceType
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="RNASequenceType";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="RNASequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.sequence.types</FONT>
+<BR>
+Class RNASequenceType</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractSequenceType</A>
+ |
+ +--<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType</A>
+ |
+ +--<B>uk.ac.man.bioinf.sequence.types.RNASequenceType</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>RNASequenceType</B><DT>extends <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></DL>
+
+<P>
+RNASequenceType.java
+
+
+ Created: Mon Nov 27 16:02:20 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: RNASequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html#instance">instance</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#elements">elements</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html#RNASequenceType()">RNASequenceType</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html#getInstance()">getInstance</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractEnumeratedSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getElementForInt(int)">getElementForInt</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html#getIntForElement(uk.ac.man.bioinf.sequence.Element)">getIntForElement</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.sequence.types.AbstractSequenceType"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getElements()">getElements</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#getName()">getName</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char)">isElement</A>, <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html#isElement(char[])">isElement</A>, <A HREF="../../../.. [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="instance"><!-- --></A><H3>
+instance</H3>
+<PRE>
+public static final <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A> <B>instance</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="RNASequenceType()"><!-- --></A><H3>
+RNASequenceType</H3>
+<PRE>
+public <B>RNASequenceType</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getInstance()"><!-- --></A><H3>
+getInstance</H3>
+<PRE>
+public static <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html">RNASequenceType</A> <B>getInstance</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="RNASequenceType.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-frame.html
new file mode 100644
index 0000000..befc182
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-frame.html
@@ -0,0 +1,67 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.types()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.types()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.sequence.types</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="DNAResidue.html" TARGET="classFrame"><I>DNAResidue</I></A>
+<BR>
+<A HREF="NucleotideResidue.html" TARGET="classFrame"><I>NucleotideResidue</I></A>
+<BR>
+<A HREF="ProteinResidue.html" TARGET="classFrame"><I>ProteinResidue</I></A>
+<BR>
+<A HREF="RNAResidue.html" TARGET="classFrame"><I>RNAResidue</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractElement.html" TARGET="classFrame">AbstractElement</A>
+<BR>
+<A HREF="AbstractEnumeratedSequenceType.html" TARGET="classFrame">AbstractEnumeratedSequenceType</A>
+<BR>
+<A HREF="AbstractSequenceType.html" TARGET="classFrame">AbstractSequenceType</A>
+<BR>
+<A HREF="AminoAcid.html" TARGET="classFrame">AminoAcid</A>
+<BR>
+<A HREF="DNANucleotide.html" TARGET="classFrame">DNANucleotide</A>
+<BR>
+<A HREF="DNASequenceType.html" TARGET="classFrame">DNASequenceType</A>
+<BR>
+<A HREF="EmptySequenceType.html" TARGET="classFrame">EmptySequenceType</A>
+<BR>
+<A HREF="ProteinSequenceType.html" TARGET="classFrame">ProteinSequenceType</A>
+<BR>
+<A HREF="RNANucleotide.html" TARGET="classFrame">RNANucleotide</A>
+<BR>
+<A HREF="RNASequenceType.html" TARGET="classFrame">RNASequenceType</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-summary.html
new file mode 100644
index 0000000..b06f4d4
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-summary.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.types()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.types()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.sequence.types
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DNAResidue.html"><I>DNAResidue</I></A></B></TD>
+<TD>DNAResidue.java
+
+ An interface to represent a DNA residue.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="NucleotideResidue.html"><I>NucleotideResidue</I></A></B></TD>
+<TD>NucleotideResidue.java
+
+ An interface to mark up nucleotide residues.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ProteinResidue.html"><I>ProteinResidue</I></A></B></TD>
+<TD>ProteinResidue.java
+
+ An interface to represent a protein residue.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="RNAResidue.html"><I>RNAResidue</I></A></B></TD>
+<TD>RNAResidue.java
+
+ An interface to represent an RNA Residue
+
+ Created: Mon Feb 28 13:02:16 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractElement.html">AbstractElement</A></B></TD>
+<TD>AbstractElement.java
+
+
+ Created: Mon Feb 28 16:10:45 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractEnumeratedSequenceType.html">AbstractEnumeratedSequenceType</A></B></TD>
+<TD>AbstractEnumeratedSequenceType.java
+
+
+ Created: Tue Jun 13 13:20:11 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractSequenceType.html">AbstractSequenceType</A></B></TD>
+<TD>AbstractSequenceType.java
+
+
+ Created: Thu Feb 17 13:02:28 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AminoAcid.html">AminoAcid</A></B></TD>
+<TD>AminoAcid.java
+
+ A class for the representation of an amino-acid.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DNANucleotide.html">DNANucleotide</A></B></TD>
+<TD>DNANucleotide.java
+
+
+ Created: Sun Sep 24 17:44:04 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="DNASequenceType.html">DNASequenceType</A></B></TD>
+<TD>DNASequenceType.java
+
+ This class represents the DNA sequence type, allowing only a set
+ of particular bases.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="EmptySequenceType.html">EmptySequenceType</A></B></TD>
+<TD>EmptySequenceType.java
+
+
+ Created: Tue Aug 1 17:22:00 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ProteinSequenceType.html">ProteinSequenceType</A></B></TD>
+<TD>ProteinSequenceType.java
+
+
+ Created: Fri Mar 3 16:12:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="RNANucleotide.html">RNANucleotide</A></B></TD>
+<TD>RNANucleotide.java
+
+ A class for the representation of RNA Nucleotides.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="RNASequenceType.html">RNASequenceType</A></B></TD>
+<TD>RNASequenceType.java
+
+
+ Created: Mon Nov 27 16:02:20 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-summary.html"><B>PREV PACKAGE</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-tree.html
new file mode 100644
index 0000000..e404d62
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/sequence/types/package-tree.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.sequence.types Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.sequence.types Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.sequence.types
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html"><B>AbstractElement</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AminoAcid.html"><B>AminoAcid</B></A> (implements uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html">ProteinResidue</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNANucleotide.html"><B>DNANucleotide</B></A> (implements uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html">DNAResidue</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNANucleotide.html"><B>RNANucleotide</B></A> (implements uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html">RNAResidue</A>)
+</UL>
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractSequenceType.html"><B>AbstractSequenceType</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.html"><B>AbstractEnumeratedSequenceType</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNASequenceType.html"><B>DNASequenceType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinSequenceType.html"><B>ProteinSequenceType</B></A><LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNASequenceType.html"><B>RNASequenceType</B [...]
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/EmptySequenceType.html"><B>EmptySequenceType</B></A> (implements uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/SequenceType.html">SequenceType</A>)
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Element.html"><B>Element</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/Residue.html"><B>Residue</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/NucleotideResidue.html"><B>NucleotideResidue</B></A><UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/DNAResidue.html"><B>DNAResidue</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/RNAResidue.html"><B>RNAResidue</B></A></UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.sequence.types.<A HREF="../../../../../../uk/ac/man/bioinf/sequence/types/ProteinResidue.html"><B>ProteinResidue</B></A></UL>
+</UL>
+</UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../uk/ac/man/bioinf/sequence/test/package-tree.html"><B>PREV</B></A>
+ <A HREF="../../../../../../uk/ac/man/bioinf/util/package-tree.html"><B>NEXT</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html b/doc/javadoc/uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html
new file mode 100644
index 0000000..87ede43
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+AbstractEnumeration.ElementIterator
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractEnumeration.ElementIterator";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeration.ElementIterator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class AbstractEnumeration.ElementIterator</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.AbstractEnumeration.ElementIterator</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></DD>
+</DL>
+<DL>
+<DT><B>Enclosing class:</B><DD><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public static class <B>AbstractEnumeration.ElementIterator</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A><DT>implements <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></DL>
+
+<P>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#AbstractEnumeration.ElementIterator(java.lang.Class)">AbstractEnumeration.ElementIterator</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#hasNext()">hasNext</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#next()">next</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html#remove()">remove</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractEnumeration.ElementIterator(java.lang.Class)"><!-- --></A><H3>
+AbstractEnumeration.ElementIterator</H3>
+<PRE>
+public <B>AbstractEnumeration.ElementIterator</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="hasNext()"><!-- --></A><H3>
+hasNext</H3>
+<PRE>
+public boolean <B>hasNext</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>hasNext</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="next()"><!-- --></A><H3>
+next</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> <B>next</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>next</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove()"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public void <B>remove</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE>remove</CODE> in interface <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeration.ElementIterator.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/AbstractEnumeration.html b/doc/javadoc/uk/ac/man/bioinf/util/AbstractEnumeration.html
new file mode 100644
index 0000000..667dcc0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/AbstractEnumeration.html
@@ -0,0 +1,415 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+AbstractEnumeration
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="AbstractEnumeration";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeration.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class AbstractEnumeration</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.AbstractEnumeration</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/types/AbstractElement.html">AbstractElement</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.html">AbstractEnumeratedModuleIdentifier</A>, <A HREF="../../../../../uk/ac/man/bioinf/apps/cinema/CinemaProperties.html">CinemaProperties</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A>, <A HREF="../../../../../uk/ac/man/bioinf/module/M [...]
+</DL>
+<HR>
+<DL>
+<DT>public abstract class <B>AbstractEnumeration</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+AbstractEnumeration.java
+
+ Provides support for Enumerated Types in Java. This class provides
+ several methods useful for all Enumerated Types including a
+ sensible printable toString method, the total
+ number of instances of a given type, an Iterator through all the
+ types, and an ordinal number running from 0 upwards for each type. <p>
+
+ This class is used by extending it with a new class which
+ <ul>
+ <li>is declared final, which prevents subclasses from
+ introducing new instances</li>
+ <li>has a private constructor</li>
+ <li>declares a public static final data member for each instance
+ that is required</li>
+ </ul>
+
+ So for example
+
+ <code>
+ <pre>
+ public final class TrafficLight extends AbstractEnumeration
+ {
+ private TrafficLight( String toString ){
+ {
+ super( toString );
+ }
+
+ public static final TrafficLight RED
+ = new TrafficLight( "TrafficLight Enumerated Type:- RED" );
+ public static final TrafficLight ORANGE
+ = new Traffic( "TrafficLight Enumerated Type:- ORANGE" );
+ public static final TrafficLight GREEN
+ = new Traffic( TrafficLight Enumerated Type:- GREEN" );
+ }
+
+ </pre>
+ </code>
+
+ Currently this class can not be serialised. Having one of the
+ subclasses implement Serializable would be a mistake as it would
+ provide an alternative route for the instances of the class to be
+ produced. This could be circumvented using the
+ replaceObject/writeObject methods introduced in the 1.2
+ serialisation spec, but I haven't got around to implementing this
+ yet!
+
+ It should be noted that there are problems in compiling this class
+ with some versions of javac. This is bug in javac (Bug ID:4157676),
+ not my code which is perfectly legal java. Jikes works
+ fine. Alternatively you can comment out the references to the ord
+ variable and do without this functionality, or make it non final,
+ in which case attempts to alter it will no longer produce compiler
+ errors as they should.
+
+ Created: Mon Feb 21 14:11:41 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: AbstractEnumeration.java,v 1.9 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static class</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected </CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#AbstractEnumeration(java.lang.String)">AbstractEnumeration</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ord"><!-- --></A><H3>
+ord</H3>
+<PRE>
+public final int <B>ord</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="AbstractEnumeration(java.lang.String)"><!-- --></A><H3>
+AbstractEnumeration</H3>
+<PRE>
+protected <B>AbstractEnumeration</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> toString)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="iterator(java.lang.Class)"><!-- --></A><H3>
+iterator</H3>
+<PRE>
+public static <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A> <B>iterator</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAllElements(java.lang.Class)"><!-- --></A><H3>
+getAllElements</H3>
+<PRE>
+public static <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A>[] <B>getAllElements</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSize(java.lang.Class)"><!-- --></A><H3>
+getSize</H3>
+<PRE>
+public static int <B>getSize</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Class.html">Class</A> cla)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toString()"><!-- --></A><H3>
+toString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>toString</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#toString()">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="AbstractEnumeration.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_class_summary">NESTED</A> | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/ArrayManipulation.html b/doc/javadoc/uk/ac/man/bioinf/util/ArrayManipulation.html
new file mode 100644
index 0000000..b08e5e0
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/ArrayManipulation.html
@@ -0,0 +1,297 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+ArrayManipulation
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ArrayManipulation";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ArrayManipulation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class ArrayManipulation</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.ArrayManipulation</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>ArrayManipulation</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ArrayManipulation.java
+
+ Just some utility functions for manipulating arrays.
+
+ Created: Thu Nov 23 14:03:06 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ArrayManipulation.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html#ArrayManipulation()">ArrayManipulation</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html#linearSearch(java.lang.Object[], java.lang.Object)">linearSearch</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] array,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> key)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html#main(java.lang.String[])">main</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html#removeFromArray(java.lang.Object[], java.lang.Object[], java.lang.Object)">removeFromArray</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] src,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] dest,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> remove)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ArrayManipulation()"><!-- --></A><H3>
+ArrayManipulation</H3>
+<PRE>
+public <B>ArrayManipulation</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="linearSearch(java.lang.Object[], java.lang.Object)"><!-- --></A><H3>
+linearSearch</H3>
+<PRE>
+public static int <B>linearSearch</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] array,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> key)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeFromArray(java.lang.Object[], java.lang.Object[], java.lang.Object)"><!-- --></A><H3>
+removeFromArray</H3>
+<PRE>
+public static void <B>removeFromArray</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] src,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] dest,
+ <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> remove)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="main(java.lang.String[])"><!-- --></A><H3>
+main</H3>
+<PRE>
+public static void <B>main</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A>[] args)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ArrayManipulation.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/Changeable.html b/doc/javadoc/uk/ac/man/bioinf/util/Changeable.html
new file mode 100644
index 0000000..0e3d598
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/Changeable.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+Changeable
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Changeable";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Changeable.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Interface Changeable</H2>
+<DL>
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public interface <B>Changeable</B></DL>
+
+<P>
+Changeable.java
+
+
+ Created: Wed Jul 19 17:26:01 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Changeable.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html#addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">addChangeListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html#removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">removeChangeListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><!-- --></A><H3>
+addChangeListener</H3>
+<PRE>
+public void <B>addChangeListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><!-- --></A><H3>
+removeChangeListener</H3>
+<PRE>
+public void <B>removeChangeListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ PREV CLASS
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Changeable.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/ChangeableEvent.html b/doc/javadoc/uk/ac/man/bioinf/util/ChangeableEvent.html
new file mode 100644
index 0000000..e03afff
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/ChangeableEvent.html
@@ -0,0 +1,250 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+ChangeableEvent
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ChangeableEvent";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeableEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.util.EventObject">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class ChangeableEvent</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">java.util.EventObject</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.ChangeableEvent</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ChangeableEvent</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></DL>
+
+<P>
+ChangeableEvent.java
+
+
+ Created: Wed Jul 19 17:29:43 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ChangeableEvent.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+<DT><B>See Also:</B><DD><A HREF="../../../../../serialized-form.html" TARGET="uk.ac.man.bioinf.util.ChangeableEvent">Serialized Form</A></DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#source">source</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html#ChangeableEvent(java.lang.Object)">ChangeableEvent</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_java.util.EventObject"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html">EventObject</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#getSource()">getSource</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ChangeableEvent(java.lang.Object)"><!-- --></A><H3>
+ChangeableEvent</H3>
+<PRE>
+public <B>ChangeableEvent</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> source)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeableEvent.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_java.util.EventObject">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#methods_inherited_from_class_java.util.EventObject">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/ChangeableListener.html b/doc/javadoc/uk/ac/man/bioinf/util/ChangeableListener.html
new file mode 100644
index 0000000..27dd8fc
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/ChangeableListener.html
@@ -0,0 +1,211 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+ChangeableListener
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ChangeableListener";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeableListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Interface ChangeableListener</H2>
+<HR>
+<DL>
+<DT>public interface <B>ChangeableListener</B></DL>
+
+<P>
+ChangeableListener.java
+
+
+ Created: Wed Jul 19 17:28:19 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ChangeableListener.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html#changeOccurred(uk.ac.man.bioinf.util.ChangeableEvent)">changeOccurred</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html">ChangeableEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.util.ChangeableEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html">ChangeableEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ExceptionHandler.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeableListener.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/ChangeableListenerSupport.html b/doc/javadoc/uk/ac/man/bioinf/util/ChangeableListenerSupport.html
new file mode 100644
index 0000000..9ceb0fd
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/ChangeableListenerSupport.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+ChangeableListenerSupport
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ChangeableListenerSupport";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeableListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class ChangeableListenerSupport</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.ChangeableListenerSupport</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ChangeableListenerSupport</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+ChangeableListenerSupport.java
+
+
+ Created: Thu Jul 20 17:58:39 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ChangeableListenerSupport.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#ChangeableListenerSupport()">ChangeableListenerSupport</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">addChangeListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#fireChangeEvent(uk.ac.man.bioinf.util.ChangeableEvent)">fireChangeEvent</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html">ChangeableEvent</A> event)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">removeChangeListener</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ChangeableListenerSupport()"><!-- --></A><H3>
+ChangeableListenerSupport</H3>
+<PRE>
+public <B>ChangeableListenerSupport</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><!-- --></A><H3>
+addChangeListener</H3>
+<PRE>
+public void <B>addChangeListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)"><!-- --></A><H3>
+removeChangeListener</H3>
+<PRE>
+public void <B>removeChangeListener</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html">ChangeableListener</A> listener)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="fireChangeEvent(uk.ac.man.bioinf.util.ChangeableEvent)"><!-- --></A><H3>
+fireChangeEvent</H3>
+<PRE>
+public void <B>fireChangeEvent</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html">ChangeableEvent</A> event)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ChangeableListenerSupport.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/CollectionPrinter.html b/doc/javadoc/uk/ac/man/bioinf/util/CollectionPrinter.html
new file mode 100644
index 0000000..0718a75
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/CollectionPrinter.html
@@ -0,0 +1,271 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+CollectionPrinter
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="CollectionPrinter";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CollectionPrinter.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class CollectionPrinter</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.CollectionPrinter</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>CollectionPrinter</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+CollectionPrinter.java
+
+
+ Created: Thu Jul 20 19:47:52 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: CollectionPrinter.java,v 1.4 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html#CollectionPrinter()">CollectionPrinter</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html#print(java.util.Map)">print</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Map.html">Map</A> map)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html#print(java.lang.Object[])">print</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] obj)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="CollectionPrinter()"><!-- --></A><H3>
+CollectionPrinter</H3>
+<PRE>
+public <B>CollectionPrinter</B>()</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="print(java.util.Map)"><!-- --></A><H3>
+print</H3>
+<PRE>
+public static void <B>print</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Map.html">Map</A> map)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="print(java.lang.Object[])"><!-- --></A><H3>
+print</H3>
+<PRE>
+public static void <B>print</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A>[] obj)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="CollectionPrinter.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/Direction.html b/doc/javadoc/uk/ac/man/bioinf/util/Direction.html
new file mode 100644
index 0000000..94f1d75
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/Direction.html
@@ -0,0 +1,315 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+Direction
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="Direction";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Direction.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class Direction</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">uk.ac.man.bioinf.util.AbstractEnumeration</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.Direction</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>Direction</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></DL>
+
+<P>
+Direction.java
+
+ EnumeratedType defining directions.
+
+ Created: Fri Jan 19 13:18:35 2001
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: Direction.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+<A NAME="nested_class_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Nested Class Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Nested classes inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html#EAST">EAST</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html#NORTH">NORTH</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html#SOUTH">SOUTH</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html#WEST">WEST</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#ord">ord</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getAllElements(java.lang.Class)">getAllElements</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#getSize(java.lang.Class)">getSize</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#iterator(java.lang.Class)">iterator</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html#toString()">toString</A></CODE></TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="NORTH"><!-- --></A><H3>
+NORTH</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A> <B>NORTH</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="EAST"><!-- --></A><H3>
+EAST</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A> <B>EAST</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="SOUTH"><!-- --></A><H3>
+SOUTH</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A> <B>SOUTH</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="WEST"><!-- --></A><H3>
+WEST</H3>
+<PRE>
+public static final <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html">Direction</A> <B>WEST</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="Direction.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: <A HREF="#nested_classes_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">NESTED</A> | <A HREF="#field_summary">FIELD</A> | CONSTR | <A HREF="#methods_inherited_from_class_uk.ac.man.bioinf.util.AbstractEnumeration">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | METHOD</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/ExceptionHandler.html b/doc/javadoc/uk/ac/man/bioinf/util/ExceptionHandler.html
new file mode 100644
index 0000000..9f51d89
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/ExceptionHandler.html
@@ -0,0 +1,212 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:38 BST 2002 -->
+<TITLE>
+ExceptionHandler
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ExceptionHandler";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Interface ExceptionHandler</H2>
+<HR>
+<DL>
+<DT>public interface <B>ExceptionHandler</B></DL>
+
+<P>
+ExceptionHandler.java
+
+ This class handles exceptions!
+
+ Created: Fri May 14 14:12:58 1999
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: ExceptionHandler.java,v 1.3 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ExceptionHandler.html#handleException(java.lang.Throwable)">handleException</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> t)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="handleException(java.lang.Throwable)"><!-- --></A><H3>
+handleException</H3>
+<PRE>
+public void <B>handleException</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Throwable.html">Throwable</A> t)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ExceptionHandler.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/IntArrayList.html b/doc/javadoc/uk/ac/man/bioinf/util/IntArrayList.html
new file mode 100644
index 0000000..814a81d
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/IntArrayList.html
@@ -0,0 +1,651 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+IntArrayList
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="IntArrayList";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntArrayList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class IntArrayList</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.IntArrayList</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>IntArrayList</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+IntArrayList.java
+
+ This class provides something akin to the ArrayList class but with
+ all the methods typed as ints, which avoids the additional bloat of
+ having to create an object for every containined integer.
+
+ Created: Fri Mar 3 23:28:54 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: IntArrayList.java,v 1.6 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#IntArrayList()">IntArrayList</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#IntArrayList(int)">IntArrayList</A></B>(int initialCapacity)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#add(int)">add</A></B>(int value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#add(int, int)">add</A></B>(int index,
+ int value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#binarySearch(int)">binarySearch</A></B>(int key)</CODE>
+
+<BR>
+ This method performs a binary search on the list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#clear()">clear</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#contains(int)">contains</A></B>(int elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#ensureCapacity(int)">ensureCapacity</A></B>(int minCapacity)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#equals(uk.ac.man.bioinf.util.IntArrayList)">equals</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> list)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#get(int)">get</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#getSubList(int, int)">getSubList</A></B>(int position,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#indexOf(int)">indexOf</A></B>(int elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#isEmpty()">isEmpty</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#lastIndexOf(int)">lastIndexOf</A></B>(int elem)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#linearSearch(int)">linearSearch</A></B>(int key)</CODE>
+
+<BR>
+ Provides a linear search.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#print()">print</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#remove(int)">remove</A></B>(int index)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#remove(int, int)">remove</A></B>(int index,
+ int length)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#set(int, int)">set</A></B>(int index,
+ int value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#size()">size</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#sort()">sort</A></B>()</CODE>
+
+<BR>
+ Sort the contents of this list.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html#toArray()">toArray</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="IntArrayList()"><!-- --></A><H3>
+IntArrayList</H3>
+<PRE>
+public <B>IntArrayList</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="IntArrayList(int)"><!-- --></A><H3>
+IntArrayList</H3>
+<PRE>
+public <B>IntArrayList</B>(int initialCapacity)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ensureCapacity(int)"><!-- --></A><H3>
+ensureCapacity</H3>
+<PRE>
+public void <B>ensureCapacity</B>(int minCapacity)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="size()"><!-- --></A><H3>
+size</H3>
+<PRE>
+public int <B>size</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="isEmpty()"><!-- --></A><H3>
+isEmpty</H3>
+<PRE>
+public boolean <B>isEmpty</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="contains(int)"><!-- --></A><H3>
+contains</H3>
+<PRE>
+public boolean <B>contains</B>(int elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="indexOf(int)"><!-- --></A><H3>
+indexOf</H3>
+<PRE>
+public int <B>indexOf</B>(int elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="lastIndexOf(int)"><!-- --></A><H3>
+lastIndexOf</H3>
+<PRE>
+public int <B>lastIndexOf</B>(int elem)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="get(int)"><!-- --></A><H3>
+get</H3>
+<PRE>
+public int <B>get</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="set(int, int)"><!-- --></A><H3>
+set</H3>
+<PRE>
+public int <B>set</B>(int index,
+ int value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="add(int)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public void <B>add</B>(int value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="add(int, int)"><!-- --></A><H3>
+add</H3>
+<PRE>
+public void <B>add</B>(int index,
+ int value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(int)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public int <B>remove</B>(int index)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="remove(int, int)"><!-- --></A><H3>
+remove</H3>
+<PRE>
+public int[] <B>remove</B>(int index,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="clear()"><!-- --></A><H3>
+clear</H3>
+<PRE>
+public void <B>clear</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getSubList(int, int)"><!-- --></A><H3>
+getSubList</H3>
+<PRE>
+public <A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> <B>getSubList</B>(int position,
+ int length)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="toArray()"><!-- --></A><H3>
+toArray</H3>
+<PRE>
+public int[] <B>toArray</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="sort()"><!-- --></A><H3>
+sort</H3>
+<PRE>
+public void <B>sort</B>()</PRE>
+<DL>
+<DD>Sort the contents of this list. Does it via a modified
+ quicksort. Which I didnt write.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="binarySearch(int)"><!-- --></A><H3>
+binarySearch</H3>
+<PRE>
+public int <B>binarySearch</B>(int key)</PRE>
+<DL>
+<DD>This method performs a binary search on the list. If you choose
+ to use this method on a list which is not guarenteed to be sorted
+ for instance by the sort method then dealing with the results is
+ distinctly your problem.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>key</CODE> - the key to search for
+<DT><B>Returns:</B><DD>the position the key is at or its insertion point.<DT><B>See Also:</B><DD><CODE>Arrays.binarySearch(int[],int)</CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="linearSearch(int)"><!-- --></A><H3>
+linearSearch</H3>
+<PRE>
+public int <B>linearSearch</B>(int key)</PRE>
+<DL>
+<DD>Provides a linear search. This works even if the list is not
+ sorted, but operates in, well linear, time.
+<P>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>key</CODE> - the key to search for
+<DT><B>Returns:</B><DD>the index or -1 if not found</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="equals(uk.ac.man.bioinf.util.IntArrayList)"><!-- --></A><H3>
+equals</H3>
+<PRE>
+public boolean <B>equals</B>(<A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html">IntArrayList</A> list)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="print()"><!-- --></A><H3>
+print</H3>
+<PRE>
+public void <B>print</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="IntArrayList.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/PackageResourceAdapter.html b/doc/javadoc/uk/ac/man/bioinf/util/PackageResourceAdapter.html
new file mode 100644
index 0000000..214e16e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/PackageResourceAdapter.html
@@ -0,0 +1,315 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+PackageResourceAdapter
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="PackageResourceAdapter";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PackageResourceAdapter.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.util.ResourceAdapter">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class PackageResourceAdapter</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">uk.ac.man.bioinf.util.ResourceAdapter</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.PackageResourceAdapter</B>
+</PRE>
+<HR>
+<DL>
+<DT>public class <B>PackageResourceAdapter</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></DL>
+
+<P>
+Looks specifically for resources in the package 'resource' that should be at the route of the Application's class path.
+ Specifically:
+ <ul>
+ <li> images should go in <code>resources.images</code>
+ <li> help documentation should go in <code>resources.helpfiles</code>
+ <li> locale data (messages, tooltips and paths to other resources such as images)
+ should go in the appropriately named properties file in <code>resources.locale</code>.
+ </ul>
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>1.0</DD>
+</DD>
+<DT><B>Author:</B><DD>C.Miller</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+</TABLE>
+ <A NAME="fields_inherited_from_class_uk.ac.man.bioinf.util.ResourceAdapter"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Fields inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#bundle">bundle</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#defaultLocale">defaultLocale</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#props">props</A></CODE></TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html#PackageResourceAdapter(java.lang.String)">PackageResourceAdapter</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyFile)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html#getHelpURL(java.lang.String)">getHelpURL</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> helpURLName)</CODE>
+
+<BR>
+ property is helpURL.<helpURLName></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html#getImageURL(java.lang.String)">getImageURL</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> imageName)</CODE>
+
+<BR>
+ property is image.<imageName> value should be path to the image</TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.ResourceAdapter"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getFile(java.lang.String)">getFile</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getMessageString(java.lang.String)">getMessageString</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getTextString(java.lang.String)">getTextString</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getToolTip(java.lang.String)">getToolTip</A>, <A HREF="../../../ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="PackageResourceAdapter(java.lang.String)"><!-- --></A><H3>
+PackageResourceAdapter</H3>
+<PRE>
+public <B>PackageResourceAdapter</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyFile)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="getHelpURL(java.lang.String)"><!-- --></A><H3>
+getHelpURL</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getHelpURL</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> helpURLName)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></CODE></B></DD>
+<DD>property is helpURL.<helpURLName>
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getHelpURL(java.lang.String)">getHelpURL</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getImageURL(java.lang.String)"><!-- --></A><H3>
+getImageURL</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getImageURL</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> imageName)</PRE>
+<DL>
+<DD><B>Description copied from class: <CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></CODE></B></DD>
+<DD>property is image.<imageName> value should be path to the image
+<P>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getImageURL(java.lang.String)">getImageURL</A></CODE> in class <CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html">ResourceAdapter</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="PackageResourceAdapter.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#fields_inherited_from_class_uk.ac.man.bioinf.util.ResourceAdapter">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/ResourceAdapter.html b/doc/javadoc/uk/ac/man/bioinf/util/ResourceAdapter.html
new file mode 100644
index 0000000..963e464
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/ResourceAdapter.html
@@ -0,0 +1,487 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:39 BST 2002 -->
+<TITLE>
+ResourceAdapter
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="ResourceAdapter";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ResourceAdapter.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class ResourceAdapter</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.ResourceAdapter</B>
+</PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html">PackageResourceAdapter</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>ResourceAdapter</B><DT>extends <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></DL>
+
+<P>
+Generic class for locating resources within an application/applet's package
+ hierarchy. Resources are defined in a locale specific property file according to
+ the conventions defined in ResourceBundle.
+ For URLs, looks up the appropriate path in the specified property file,
+ and then uses that to retrieve a pointer to it.
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>1.0</DD>
+</DD>
+<DT><B>Author:</B><DD>C.Miller</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+<A NAME="field_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Field Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/ResourceBundle.html">ResourceBundle</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#bundle">bundle</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Locale.html">Locale</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#defaultLocale">defaultLocale</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#props">props</A></B></CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#ResourceAdapter()">ResourceAdapter</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#ResourceAdapter(java.lang.String)">ResourceAdapter</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyFile)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getFile(java.lang.String)">getFile</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> fileDescriptor)</CODE>
+
+<BR>
+ property is file.<fileDescriptor> value should be path to the image</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getHelpURL(java.lang.String)">getHelpURL</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> helpURLName)</CODE>
+
+<BR>
+ property is helpURL.<helpURLName></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getImageURL(java.lang.String)">getImageURL</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> imageName)</CODE>
+
+<BR>
+ property is image.<imageName> value should be path to the image</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getMessageString(java.lang.String)">getMessageString</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> messageName)</CODE>
+
+<BR>
+ property is message.<messageName></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getTextString(java.lang.String)">getTextString</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> descriptor)</CODE>
+
+<BR>
+ property is string.<descriptor> value should be a String</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getToolTip(java.lang.String)">getToolTip</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> tooltipName)</CODE>
+
+<BR>
+ property is tooltip.<tooltipName></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A></CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#getURL(java.lang.String)">getURL</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> URLDescriptor)</CODE>
+
+<BR>
+ property is url.<URLDescriptor> value should be a URL</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>protected void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html#init()">init</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang [...]
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+<A NAME="field_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Field Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="defaultLocale"><!-- --></A><H3>
+defaultLocale</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Locale.html">Locale</A> <B>defaultLocale</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="bundle"><!-- --></A><H3>
+bundle</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/ResourceBundle.html">ResourceBundle</A> <B>bundle</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+<HR>
+
+<A NAME="props"><!-- --></A><H3>
+props</H3>
+<PRE>
+protected <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>props</B></PRE>
+<DL>
+<DL>
+</DL>
+</DL>
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="ResourceAdapter()"><!-- --></A><H3>
+ResourceAdapter</H3>
+<PRE>
+public <B>ResourceAdapter</B>()</PRE>
+<DL>
+</DL>
+<HR>
+
+<A NAME="ResourceAdapter(java.lang.String)"><!-- --></A><H3>
+ResourceAdapter</H3>
+<PRE>
+public <B>ResourceAdapter</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> propertyFile)
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="init()"><!-- --></A><H3>
+init</H3>
+<PRE>
+protected void <B>init</B>()
+ throws <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></PRE>
+<DL>
+<DD><DL>
+
+<DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/IOException.html">IOException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getMessageString(java.lang.String)"><!-- --></A><H3>
+getMessageString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getMessageString</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> messageName)</PRE>
+<DL>
+<DD>property is message.<messageName>
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getToolTip(java.lang.String)"><!-- --></A><H3>
+getToolTip</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getToolTip</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> tooltipName)</PRE>
+<DL>
+<DD>property is tooltip.<tooltipName>
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getHelpURL(java.lang.String)"><!-- --></A><H3>
+getHelpURL</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getHelpURL</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> helpURLName)</PRE>
+<DL>
+<DD>property is helpURL.<helpURLName>
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getImageURL(java.lang.String)"><!-- --></A><H3>
+getImageURL</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getImageURL</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> imageName)</PRE>
+<DL>
+<DD>property is image.<imageName> value should be path to the image
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getFile(java.lang.String)"><!-- --></A><H3>
+getFile</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/File.html">File</A> <B>getFile</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> fileDescriptor)</PRE>
+<DL>
+<DD>property is file.<fileDescriptor> value should be path to the image
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getURL(java.lang.String)"><!-- --></A><H3>
+getURL</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/net/URL.html">URL</A> <B>getURL</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> URLDescriptor)</PRE>
+<DL>
+<DD>property is url.<URLDescriptor> value should be a URL
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getTextString(java.lang.String)"><!-- --></A><H3>
+getTextString</H3>
+<PRE>
+public <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> <B>getTextString</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/String.html">String</A> descriptor)</PRE>
+<DL>
+<DD>property is string.<descriptor> value should be a String
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html"><B>NEXT CLASS</B></A></FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="ResourceAdapter.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html b/doc/javadoc/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html
new file mode 100644
index 0000000..1127c1e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html
@@ -0,0 +1,350 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:13:40 BST 2002 -->
+<TITLE>
+SequenceAlignmentToChangeableAdaptor
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="SequenceAlignmentToChangeableAdaptor";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentToChangeableAdaptor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<!-- ======== START OF CLASS DATA ======== -->
+<H2>
+<FONT SIZE="-1">
+uk.ac.man.bioinf.util</FONT>
+<BR>
+Class SequenceAlignmentToChangeableAdaptor</H2>
+<PRE>
+<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">java.lang.Object</A>
+ |
+ +--<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html">uk.ac.man.bioinf.util.ChangeableListenerSupport</A>
+ |
+ +--<B>uk.ac.man.bioinf.util.SequenceAlignmentToChangeableAdaptor</B>
+</PRE>
+<DL>
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html">Changeable</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventListener.html">EventListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></DD>
+</DL>
+<HR>
+<DL>
+<DT>public class <B>SequenceAlignmentToChangeableAdaptor</B><DT>extends <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A><DT>implements <A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html">Changeable</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></DL>
+
+<P>
+SequenceAlignmentToChangeableAdaptor.java
+
+
+ Created: Thu Jul 20 17:57:44 2000
+<P>
+
+<P>
+<DL>
+<DT><B>Version:</B><DD>$Id: SequenceAlignmentToChangeableAdaptor.java,v 1.2 2001/04/11 17:04:43 lord Exp $</DD>
+</DD>
+<DT><B>Author:</B><DD>Phillip Lord</DD>
+</DD>
+</DL>
+<HR>
+
+<P>
+<!-- ======== NESTED CLASS SUMMARY ======== -->
+
+
+<!-- =========== FIELD SUMMARY =========== -->
+
+
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->
+
+<A NAME="constructor_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Constructor Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#SequenceAlignmentToChangeableAdaptor(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)">SequenceAlignmentToChangeableAdaptor</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+
+<!-- ========== METHOD SUMMARY =========== -->
+
+<A NAME="method_summary"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Method Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</CODE>
+
+<BR>
+ method signalled after a change has occured to a multiple alignment</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</CODE>
+
+<BR>
+ Method called when a change occurs</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> object)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> int</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html#hashCode()">hashCode</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.ChangeableListenerSupport"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html">ChangeableListenerSupport</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">addChangeListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#fireChangeEvent(uk.ac.man.bioinf.util.ChangeableEvent)">fireChangeEvent</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html#removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">removeChangeListener</A></ [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#clone()">clone</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#finalize()">finalize</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#getClass()">getClass</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#notify()">notify</A>, <A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#not [...]
+</TR>
+</TABLE>
+ <A NAME="methods_inherited_from_class_uk.ac.man.bioinf.util.Changeable"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TD><B>Methods inherited from interface uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html">Changeable</A></B></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><CODE><A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html#addChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">addChangeListener</A>, <A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html#removeChangeListener(uk.ac.man.bioinf.util.ChangeableListener)">removeChangeListener</A></CODE></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<!-- ============ FIELD DETAIL =========== -->
+
+
+<!-- ========= CONSTRUCTOR DETAIL ======== -->
+
+<A NAME="constructor_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Constructor Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="SequenceAlignmentToChangeableAdaptor(uk.ac.man.bioinf.sequence.alignment.SequenceAlignment)"><!-- --></A><H3>
+SequenceAlignmentToChangeableAdaptor</H3>
+<PRE>
+public <B>SequenceAlignmentToChangeableAdaptor</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.html">SequenceAlignment</A> alignment)</PRE>
+<DL>
+</DL>
+
+<!-- ============ METHOD DETAIL ========== -->
+
+<A NAME="method_detail"><!-- --></A>
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=1><FONT SIZE="+2">
+<B>Method Detail</B></FONT></TD>
+</TR>
+</TABLE>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceEvent.html">SequenceEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></B></DD>
+<DD>Method called when a change occurs
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html#changeOccurred(uk.ac.man.bioinf.sequence.event.SequenceEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/event/SequenceListener.html">SequenceListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - </DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)"><!-- --></A><H3>
+changeOccurred</H3>
+<PRE>
+public void <B>changeOccurred</B>(<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.html">AlignmentEvent</A> event)</PRE>
+<DL>
+<DD><B>Description copied from interface: <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></B></DD>
+<DD>method signalled after a change has occured to a multiple alignment
+<P>
+<DD><DL>
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html#changeOccurred(uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent)">changeOccurred</A></CODE> in interface <CODE><A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A></CODE></DL>
+</DD>
+<DD><DL>
+<DT><B>Parameters:</B><DD><CODE>event</CODE> - the event type</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="hashCode()"><!-- --></A><H3>
+hashCode</H3>
+<PRE>
+public int <B>hashCode</B>()</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#hashCode()">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="equals(java.lang.Object)"><!-- --></A><H3>
+equals</H3>
+<PRE>
+public boolean <B>equals</B>(<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A> object)</PRE>
+<DL>
+<DD><DL>
+<DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html#equals(java.lang.Object)">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html">Object</A></CODE></DL>
+</DD>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<!-- ========= END OF CLASS DATA ========= -->
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html"><B>PREV CLASS</B></A>
+ NEXT CLASS</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="SequenceAlignmentToChangeableAdaptor.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+<TR>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/package-frame.html b/doc/javadoc/uk/ac/man/bioinf/util/package-frame.html
new file mode 100644
index 0000000..de3ae8b
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/package-frame.html
@@ -0,0 +1,67 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.util()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.util()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+<FONT size="+1" CLASS="FrameTitleFont">
+<A HREF="../../../../../uk/ac/man/bioinf/util/package-summary.html" TARGET="classFrame">uk.ac.man.bioinf.util</A></FONT>
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Interfaces</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="Changeable.html" TARGET="classFrame"><I>Changeable</I></A>
+<BR>
+<A HREF="ChangeableListener.html" TARGET="classFrame"><I>ChangeableListener</I></A>
+<BR>
+<A HREF="ExceptionHandler.html" TARGET="classFrame"><I>ExceptionHandler</I></A></FONT></TD>
+</TR>
+</TABLE>
+
+
+<TABLE BORDER="0" WIDTH="100%">
+<TR>
+<TD NOWRAP><FONT size="+1" CLASS="FrameHeadingFont">
+Classes</FONT>
+<FONT CLASS="FrameItemFont">
+<BR>
+<A HREF="AbstractEnumeration.html" TARGET="classFrame">AbstractEnumeration</A>
+<BR>
+<A HREF="AbstractEnumeration.ElementIterator.html" TARGET="classFrame">AbstractEnumeration.ElementIterator</A>
+<BR>
+<A HREF="ArrayManipulation.html" TARGET="classFrame">ArrayManipulation</A>
+<BR>
+<A HREF="ChangeableEvent.html" TARGET="classFrame">ChangeableEvent</A>
+<BR>
+<A HREF="ChangeableListenerSupport.html" TARGET="classFrame">ChangeableListenerSupport</A>
+<BR>
+<A HREF="CollectionPrinter.html" TARGET="classFrame">CollectionPrinter</A>
+<BR>
+<A HREF="Direction.html" TARGET="classFrame">Direction</A>
+<BR>
+<A HREF="IntArrayList.html" TARGET="classFrame">IntArrayList</A>
+<BR>
+<A HREF="PackageResourceAdapter.html" TARGET="classFrame">PackageResourceAdapter</A>
+<BR>
+<A HREF="ResourceAdapter.html" TARGET="classFrame">ResourceAdapter</A>
+<BR>
+<A HREF="SequenceAlignmentToChangeableAdaptor.html" TARGET="classFrame">SequenceAlignmentToChangeableAdaptor</A></FONT></TD>
+</TR>
+</TABLE>
+
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/package-summary.html b/doc/javadoc/uk/ac/man/bioinf/util/package-summary.html
new file mode 100644
index 0000000..3281ad6
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/package-summary.html
@@ -0,0 +1,229 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.util()
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.util()";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/package-summary.html"><B>PREV PACKAGE</B></A>
+ NEXT PACKAGE</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<H2>
+Package uk.ac.man.bioinf.util
+</H2>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Interface Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Changeable.html"><I>Changeable</I></A></B></TD>
+<TD>Changeable.java
+
+
+ Created: Wed Jul 19 17:26:01 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ChangeableListener.html"><I>ChangeableListener</I></A></B></TD>
+<TD>ChangeableListener.java
+
+
+ Created: Wed Jul 19 17:28:19 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ExceptionHandler.html"><I>ExceptionHandler</I></A></B></TD>
+<TD>ExceptionHandler.java
+
+ This class handles exceptions!
+
+ Created: Fri May 14 14:12:58 1999</TD>
+</TR>
+</TABLE>
+
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TD COLSPAN=2><FONT SIZE="+2">
+<B>Class Summary</B></FONT></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractEnumeration.html">AbstractEnumeration</A></B></TD>
+<TD>AbstractEnumeration.java
+
+ Provides support for Enumerated Types in Java.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="AbstractEnumeration.ElementIterator.html">AbstractEnumeration.ElementIterator</A></B></TD>
+<TD> </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ArrayManipulation.html">ArrayManipulation</A></B></TD>
+<TD>ArrayManipulation.java
+
+ Just some utility functions for manipulating arrays.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ChangeableEvent.html">ChangeableEvent</A></B></TD>
+<TD>ChangeableEvent.java
+
+
+ Created: Wed Jul 19 17:29:43 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ChangeableListenerSupport.html">ChangeableListenerSupport</A></B></TD>
+<TD>ChangeableListenerSupport.java
+
+
+ Created: Thu Jul 20 17:58:39 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="CollectionPrinter.html">CollectionPrinter</A></B></TD>
+<TD>CollectionPrinter.java
+
+
+ Created: Thu Jul 20 19:47:52 2000</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="Direction.html">Direction</A></B></TD>
+<TD>Direction.java
+
+ EnumeratedType defining directions.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="IntArrayList.html">IntArrayList</A></B></TD>
+<TD>IntArrayList.java
+
+ This class provides something akin to the ArrayList class but with
+ all the methods typed as ints, which avoids the additional bloat of
+ having to create an object for every containined integer.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PackageResourceAdapter.html">PackageResourceAdapter</A></B></TD>
+<TD>Looks specifically for resources in the package 'resource' that should be at the route of the Application's class path.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="ResourceAdapter.html">ResourceAdapter</A></B></TD>
+<TD>Generic class for locating resources within an application/applet's package
+ hierarchy.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="SequenceAlignmentToChangeableAdaptor.html">SequenceAlignmentToChangeableAdaptor</A></B></TD>
+<TD>SequenceAlignmentToChangeableAdaptor.java
+
+
+ Created: Thu Jul 20 17:57:44 2000</TD>
+</TR>
+</TABLE>
+
+
+<P>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/package-summary.html"><B>PREV PACKAGE</B></A>
+ NEXT PACKAGE</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-summary.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/javadoc/uk/ac/man/bioinf/util/package-tree.html b/doc/javadoc/uk/ac/man/bioinf/util/package-tree.html
new file mode 100644
index 0000000..47c1f7e
--- /dev/null
+++ b/doc/javadoc/uk/ac/man/bioinf/util/package-tree.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
+<!--NewPage-->
+<HTML>
+<HEAD>
+<!-- Generated by javadoc on Sat Apr 20 16:12:13 BST 2002 -->
+<TITLE>
+uk.ac.man.bioinf.util Class Hierarchy
+</TITLE>
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../../stylesheet.css" TITLE="Style">
+</HEAD>
+<SCRIPT>
+function asd()
+{
+parent.document.title="uk.ac.man.bioinf.util Class Hierarchy";
+}
+</SCRIPT>
+<BODY BGCOLOR="white" onload="asd();">
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_top"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_top_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/package-tree.html"><B>PREV</B></A>
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+<CENTER>
+<H2>
+Hierarchy For Package uk.ac.man.bioinf.util
+</H2>
+</CENTER>
+<DL>
+<DT><B>Package Hierarchies:</B><DD><A HREF="../../../../../overview-tree.html">All Packages</A></DL>
+<HR>
+<H2>
+Class Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">class java.lang.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/lang/Object.html"><B>Object</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.html"><B>AbstractEnumeration</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/Direction.html"><B>Direction</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/AbstractEnumeration.ElementIterator.html"><B>AbstractEnumeration.ElementIterator</B></A> (implements java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/Iterator.html">Iterator</A>)
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ArrayManipulation.html"><B>ArrayManipulation</B></A><LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListenerSupport.html"><B>ChangeableListenerSupport</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.html"><B>SequenceAlignmentToChangeableAdaptor</B></A> (implements uk.ac.man.bioinf.sequence.alignment.event.<A HREF="../../../../../uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.html">AlignmentListener</A>, uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html">Changeable</A>, uk.ac.man.bioinf.sequence.event.<A HREF=" [...]
+</UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/CollectionPrinter.html"><B>CollectionPrinter</B></A><LI TYPE="circle">class java.util.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/util/EventObject.html"><B>EventObject</B></A> (implements java.io.<A HREF="http://java.sun.com/products/jdk/1.2/docs/api/java/io/Serializable.html">Serializable</A>)
+<UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableEvent.html"><B>ChangeableEvent</B></A></UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/IntArrayList.html"><B>IntArrayList</B></A><LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ResourceAdapter.html"><B>ResourceAdapter</B></A><UL>
+<LI TYPE="circle">class uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/PackageResourceAdapter.html"><B>PackageResourceAdapter</B></A></UL>
+</UL>
+</UL>
+<H2>
+Interface Hierarchy
+</H2>
+<UL>
+<LI TYPE="circle">interface uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/Changeable.html"><B>Changeable</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ChangeableListener.html"><B>ChangeableListener</B></A><LI TYPE="circle">interface uk.ac.man.bioinf.util.<A HREF="../../../../../uk/ac/man/bioinf/util/ExceptionHandler.html"><B>ExceptionHandler</B></A></UL>
+<HR>
+
+<!-- ========== START OF NAVBAR ========== -->
+<A NAME="navbar_bottom"><!-- --></A>
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0">
+<TR>
+<TD COLSPAN=3 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">
+<A NAME="navbar_bottom_firstrow"><!-- --></A>
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3">
+ <TR ALIGN="center" VALIGN="top">
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Tree</B></FONT> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../index-all.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>
+ </TR>
+</TABLE>
+</TD>
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
+</EM>
+</TD>
+</TR>
+
+<TR>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../uk/ac/man/bioinf/sequence/types/package-tree.html"><B>PREV</B></A>
+ NEXT</FONT></TD>
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
+ <A HREF="../../../../../index.html" TARGET="_top"><B>FRAMES</B></A>
+ <A HREF="package-tree.html" TARGET="_top"><B>NO FRAMES</B></A>
+
+<SCRIPT>
+ <!--
+ if(window==top) {
+ document.writeln('<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>');
+ }
+ //-->
+</SCRIPT>
+<NOSCRIPT>
+<A HREF="../../../../../allclasses-noframe.html" TARGET=""><B>All Classes</B></A>
+</NOSCRIPT>
+</FONT></TD>
+</TR>
+</TABLE>
+<!-- =========== END OF NAVBAR =========== -->
+
+<HR>
+
+</BODY>
+</HTML>
diff --git a/doc/sequence/alignment.sgml b/doc/sequence/alignment.sgml
new file mode 100644
index 0000000..e5154fa
--- /dev/null
+++ b/doc/sequence/alignment.sgml
@@ -0,0 +1,136 @@
+
+<section>
+ <title>Sequence Alignments</title>
+
+ <section>
+ <title>Design</title>
+
+ <para>Most of the work for modelling a sequence alignment has
+ already been done in the shape of the
+ <link linkend="gappable.and.editable">Gapped Sequence</link>.
+ From here it becomes relatively easy to model
+ an alignment, as a simple list of GappedSequences, with the
+ addition of an event model for describing those changes in the
+ Sequences which are a part of the alignment. </para>
+
+ <para>The SequenceAlignment interface therefore contains the
+ following methods for adding and removing Sequences
+
+ <programlisting>
+ public void addSequence(GappedSequence seq, int inset)
+ throws AlignmentVetoException;
+
+ public GappedSequence removeSequence(int seqIndex)
+ throws AlignmentVetoException;
+ </programlisting>
+
+ Insets have been provided so that all the sequences do not have
+ to start at the same point. The alternative was to add Gaps at
+ the beginning of the GappedSequences. This also means that we
+ need methods to manipulate the insets separately. These are
+
+ <programlisting>
+ public void setInset(int seqIndex, int size) throws AlignmentVetoException;
+
+ public int getInset(int seqIndex);
+ </programlisting>
+ </para>
+
+ <para>Next we have a series of informational methods. As with
+ Sequences, it seems appropriate to enforce "type-checking" on
+ alignments as normally we will want to align sequencs of the
+ same type. We use the same mechanism as with Sequences.
+
+ <programlisting>
+ public SequenceType getSequenceType();
+ </programlisting>
+
+ We also need mechanisms to access the individual sequences,
+ their overall size, and number.
+
+ <programlisting>
+ public GappedSequence getSequenceAt(int index) throws NoSuchSequenceException;
+
+ public int getSequenceIndex(GappedSequence seq);
+
+ public int getNumberSequences();
+
+ public int getLength();
+ </programlisting>
+ </para>
+ </section>
+
+ <section>
+ <title>Events</title>
+
+ <para>The SequenceAlignment is also required to signal
+ events. These have been classifed into two groups, namely the
+ <classname>AlignmentEvents</classname>, which describe changes
+ such as the addition or removal of Sequences. These are defined
+ in the <classname>AlignmentEventProvider</classname>
+ interface. </para>
+
+ <para>The second type of event is the
+ <classname>SequenceEvent</classname> which are the events
+ signalled by the <classname>GappedSequence</classname>
+ itself. In order to simply the process of listening to all its
+ sequences an alignment acts as a proxy for all of its
+ sequences. It implements the
+ <classname>SequenceEventProvider</classname> interface, and
+ any events which the individual
+ <classname>GappedSequences</classname> signal will be passed
+ onwards. This means that SequenceListeners do not have to listen
+ for addition and removal of Sequences, and add and remove
+ themselves as listeners when this happens. </para>
+ </section>
+
+ <section>
+ <title>The default implementation</title>
+
+ <para>As with the Sequence implementation the SequenceAlignment
+ has uses the standard Java API's to store its data, in this case
+ an <classname>ArrayList</classname>. This class by default
+ listens directly to all of the sequences of which it is
+ comprised and uses these to determine when length changes
+ occur.
+ </para>
+ </section>
+
+ <section>
+ <title>Support classes</title>
+
+ <para>Several support classes have been added to make dealing with
+ <classname>SequenceAlignment</classname> simpler. The first of
+ these is the <classname>AlignmentColumn</classname>. Because the
+ individual <classname>GappedSequences</classname> have staggered
+ start points dealing with an individual column requires
+ calculating the inset of a sequence, and then checking the size
+ to see whether the column is before or after the sequence. The
+ <classname>AlignmentColumn</classname> does this work.</para>
+
+ <![%draft;[
+ <para>
+ <emphasis>We really need to move the geom package into the
+ alignment package. This is a bit of a pain in the ass, but its
+ just not appropriate at the moment.</emphasis>
+ </para>
+ ]]>
+
+ <para>Secondly there are a series of classes i4n the
+ "geom" package which are designed to refer to regions
+ of sequences. This package is modelled on the equivalent classes
+ in the java.awt package, namely <classname>Point</classname>,
+ <classname>Dimension</classname>, and
+ <classname>Rectangle</classname>.</para>
+ </section>
+</section>
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
+
+
diff --git a/doc/sequence/conclusions.sgml b/doc/sequence/conclusions.sgml
new file mode 100644
index 0000000..e3fd69f
--- /dev/null
+++ b/doc/sequence/conclusions.sgml
@@ -0,0 +1,19 @@
+<section>
+ <title>Conclusions</title>
+
+ <para>We believe that the &seqapi; addresses the problem of
+ representing biological sequences within the Java langauge. At the
+ current time this API has been used within one major project and
+ has been found to be adaptable and comprehensive within that
+ environment. As such we believe that it could form the basis of a
+ generic API for bioinformatics within Java</para>
+</section>
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
+
diff --git a/doc/sequence/elementandtype.sgml b/doc/sequence/elementandtype.sgml
new file mode 100644
index 0000000..f209c84
--- /dev/null
+++ b/doc/sequence/elementandtype.sgml
@@ -0,0 +1,174 @@
+
+<section>
+ <title>Implementation of the &seqapi;</title>
+
+ <section>
+ <title>The list elements</title>
+
+ <para>It is common in bioinformatics to represent a biological
+ sequence as a series of characters, or a string. This has the
+ several advantages, the main advantages being simplicity. Also
+ many languages have special facilities for dealing with
+ strings. And finally characters are printable which can make
+ help during development. The facilities that Java provides
+ however are not very advanced however, so this advantage is
+ lessened. </para>
+
+ <para>The main disadvantage with using characters though is that
+ they are of limited number (Java actually has 65536 of them, but
+ of these are unprintable, or not readily identifiable from each
+ other when printed). It is for this reason amoung others that
+ "type" errors (is this 'C' a cysteine, or a cytosine?)
+ become easy to make. Additionally using characters makes it
+ impossible to attach other information (about the molecular
+ mass) to the element, necessitating lookup tables. There is also
+ an additional problem specific to Java which is that the
+ "char" datatype is "primitive", i.e. not a
+ first class Java object. This means that it can not be passed or
+ returned as an Object parameter. This means that it can not be
+ used by any of the standard Java data structures without using
+ an "Character" object wrapper. During coding this
+ defeats any advantages of simplicity.</para>
+
+ <para>For these reasons we have implemented the <classname>Element
+ </classname> as a Java object. This interface implements just a
+ single method...
+
+ <programlisting>
+ public interface Element
+ {
+ public char toChar();
+ }// Element
+ </programlisting>
+
+ This method helps to retain one of the advantages of using
+ characters which is that is provides a natural way of printing
+ sequences, without any of the associated disadvantages, as the
+ char representation of an
+ <classname>Element</classname> is not required to be
+ unique.
+ </para>
+
+ <para>We have extended <classname>Element</classname> in
+ two ways. Firstly with the
+ <classname>Residue</</classname> interface. This is a
+ simple "tagging" interface with no methods. Its the
+ root interface for all Objects which are to represent residues,
+ as opposed to Gaps. These are represented by their own class,
+ called unsurprisingly <classname>Gap</classname>. This has been
+ implemented using the "Singleton" design pattern.
+
+ <programlisting>
+ public class Gap extends Element
+ {
+ private Gap()
+ {}
+
+ public char toChar()
+ {
+ return '-';
+ }
+
+ public String toString()
+ {
+ return "Gap Element";
+ }
+
+ public static final Gap gap = new Gap();
+ }
+ </programlisting>
+
+ As well as <classname>Gap</classname> we have also provided
+ default implementations of common
+ <classname>Element's</classname>. For example the
+ <classname>DNAResidue</classname> extends Residue directly
+ providing a tagging interface, and this is then extended by
+ <classname>DNANucleotide</classname>. This is implemented as an
+ Enumerated Type which in Java is provided by a variation on the
+ theme of the Singleton design pattern
+
+ <programlisting>
+
+ public class DNANucleotide extends AbstractElement
+ implements DNAResidue
+ {
+ private String full;
+ private DNANucleotide ( char singleChar, String full, String toString )
+ {
+ super( toString, singleChar );
+ this.full = full;
+ }
+
+ public static final DNANucleotide ADENOSINE =
+ new DNANucleotide('A', "Adenosine", "DNANucleotide Adenosine");
+ public static final DNANucleotide GUANINE =
+ new DNANucleotide('G', "Guanine", "DNANucleotide Guanine");
+ public static final DNANucleotide CYTOSINE =
+ new DNANucleotide('C', "Cytosine", "DNANucleotide Cytosine");
+ public static final DNANucleotide THIAMINE =
+ new DNANucleotide('T', "Thiamine", "DNANucleotide ThIAmine");
+ }
+ </programlisting>
+
+ The super class <classname>AbstractElement</classname> provides
+ several methods for managing enumerated types.</para>
+ </section>
+
+ <section>
+ <title>Sequence types. A collection of Elements</title>
+
+ <para>One of the requirements for the &seqapi; was to provide a
+ degree of "type-checking" for sequences to prevent a
+ sequence of an inappropriate type being added to a Sequence. The
+ most obvious way of doing this in Java would have been to use
+ the type system. Therefore a DNA sequence would have for
+ instance a method
+ <function>DNANucleotide getElementAt( int index )</function>.
+ The problem is that we would like all Sequences to share an
+ common inheritance, so that classes which do not care about the
+ type of the sequence can deal generically with all sequences. In
+ Java we could do this by giving the super class a method
+ <function>Element getElementAt( int index )</function>. Sadly
+ this is illegal in Java, as this method has the same signature
+ as one in a subclass, but a different return type. There are
+ languages which can support this kind of type system. The
+ language feature known as "parameterised typing" would
+ for instance have served nicely. Its rather depressing to note
+ that the foreword of version 1.0 of the Java Language
+ Specification suggests that this is a good language feature
+ which might be added someday. Sadly it is not here now, or we
+ would have used it in this API. At the current time though we
+ have had to conclude that it is not possible to use Java's type
+ system to provide compile time safety.
+ </para>
+
+ <para>Failing compile time safety we investigated the possibility
+ of providing a fail fast runtime safety check. For this we need
+ to be able to tell if an Element was a valid part of a given
+ Sequence. The class <classname>SequenceType</classname>This
+ provides one function of critical importance...
+
+ <programlisting>
+ public interface SequenceType
+ {
+ public boolean isElement( Element element );
+ }
+ </programlisting>
+
+ as well as a number of other convienience and informational
+ functions</para>
+
+ <para>This class is used to implement all of the "type
+ checks" that are performed in the Sequence class. </para>
+
+ </section>
+</section>
+
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
diff --git a/doc/sequence/implementation.sgml b/doc/sequence/implementation.sgml
new file mode 100644
index 0000000..f72dc4d
--- /dev/null
+++ b/doc/sequence/implementation.sgml
@@ -0,0 +1,172 @@
+
+<section>
+ <title>Implementation of the &seqapi;</title>
+
+ <section>
+ <title>The list elements</title>
+
+ <para>It is common in bioinformatics to represent a biological
+ sequence as a series of characters, or a string. This has the
+ several advantages, the main advantages being simplicity. Also
+ many languages have special facilities for dealing with
+ strings. And finally characters are printable which can make
+ help during development. The facilities that Java provides
+ however are not very advanced however, so this advantage is
+ lessened. </para>
+
+ <para>The main disadvantage with using characters though is that
+ they are of limited number (Java actually has 65536 of them, but
+ of these are unprintable, or not readily identifiable from each
+ other when printed). It is for this reason amoung others that
+ "type" errors (is this 'C' a cysteine, or a cytosine?)
+ become easy to make. Additionally using characters makes it
+ impossible to attach other information (about the molecular
+ mass) to the element, necessitating lookup tables. There is also
+ an additional problem specific to Java which is that the
+ "char" datatype is "primitive", i.e. not a
+ first class Java object. This means that it can not be passed or
+ returned as an Object parameter. This means that it can not be
+ used by any of the standard Java data structures without using
+ an "Character" object wrapper. During coding this
+ defeats any advantages of simplicity.</para>
+
+ <para>For these reasons we have implemented the <classname>Element
+ </classname> as a Java object. This interface implements just a
+ single method...
+
+ <programlisting>
+ public interface Element
+ {
+ public char toChar();
+ }// Element
+ </programlisting>
+
+ This method helps to retain one of the advantages of using
+ characters which is that is provides a natural way of printing
+ sequences, without any of the associated disadvantages, as the
+ char representation of an
+ <classname>Element</classname> is not required to be
+ unique.
+ </para>
+
+ <para>We have extended <classname>Element</classname> in
+ two ways. Firstly with the
+ <classname>Residue</</classname> interface. This is a
+ simple "tagging" interface with no methods. Its the
+ root interface for all Objects which are to represent residues,
+ as opposed to Gaps. These are represented by their own class,
+ called unsurprisingly <classname>Gap</classname>. This has been
+ implemented using the "Singleton" design pattern.
+
+ <programlisting>
+ public class Gap extends Element
+ {
+ private Gap()
+ {}
+
+ public char toChar()
+ {
+ return '-';
+ }
+
+ public String toString()
+ {
+ return "Gap Element";
+ }
+
+ public static final Gap gap = new Gap();
+ }
+ </programlisting>
+
+ As well as <classname>Gap</classname> we have also provided
+ default implementations of common
+ <classname>Element's</classname>. For example the
+ <classname>DNAResidue</classname> extends Residue directly
+ providing a tagging interface, and this is then extended by
+ <classname>DNANucleotide</classname>. This is implemented as an
+ Enumerated Type which in Java is provided by a variation on the
+ theme of the Singleton design pattern
+
+ <programlisting>
+
+ public class DNANucleotide extends AbstractElement
+ implements DNAResidue
+ {
+ private String full;
+ private DNANucleotide ( char singleChar, String full, String toString )
+ {
+ super( toString, singleChar );
+ this.full = full;
+ }
+
+ public static final DNANucleotide ADENOSINE =
+ new DNANucleotide('A', "Adenosine", "DNANucleotide Adenosine");
+ public static final DNANucleotide GUANINE =
+ new DNANucleotide('G', "Guanine", "DNANucleotide Guanine");
+ public static final DNANucleotide CYTOSINE =
+ new DNANucleotide('C', "Cytosine", "DNANucleotide Cytosine");
+ public static final DNANucleotide THIAMINE =
+ new DNANucleotide('U', "Uracil", "DNANucleotide ThIAmine");
+ }
+ </programlisting>
+
+ The super class <classname>AbstractElement</classname> provides
+ several methods for managing enumerated types.</para>
+ </section>
+
+ <section>
+ <title>Sequence types. A collection of Elements</title>
+
+ <para>One of the requirements for the &seqapi; was to provide a
+ degree of "type-checking" for sequences to prevent a
+ sequence of an inappropriate type being added to a Sequence. The
+ most obvious way of doing this in Java would have been to use
+ the type system. Therefore a DNA sequence would have for
+ instance a method
+ <function>DNANucleotide getElementAt( int index )</function>.
+ The problem is that we would like all Sequences to share an
+ common inheritance, so that classes which do not care about the
+ type of the sequence can deal generically with all sequences. In
+ Java we could do this by giving the super class a method
+ <function>Element getElementAt( int index )</function>. Sadly
+ this is illegal in Java, as this method has the same signature
+ as one in a subclass, but a different return type. There are
+ languages which can support this kind of type system. The
+ language feature known as "parameterised typing" would
+ for instance have served nicely. Its rather depressing to note
+ that the foreword of version 1.0 of the Java Language
+ Specification suggests that this is a good language feature
+ which might be added someday. Sadly it is not here now, or we
+ would have used it in this API. At the current time though we
+ have had to conclude that it is not possible to use Java's type
+ system to provide compile time safety.
+ </para>
+
+ <para>Failing compile time safety we investigated the possibility
+ of providing a fail fast runtime safety check. For this we need
+ to be able to tell if an Element was a valid part of a given
+ Sequence. The class <classname>SequenceType</classname>This
+ provides one function of critical importance...
+
+ <programlisting>
+ public interface SequenceType
+ {
+ public boolean isElement( Element element );
+ }
+ </programlisting>
+
+ as well as a number of other convienience and informational
+ functions</para>
+
+
+ </section>
+</section>
+
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
diff --git a/doc/sequence/intro.sgml b/doc/sequence/intro.sgml
new file mode 100644
index 0000000..bb8337d
--- /dev/null
+++ b/doc/sequence/intro.sgml
@@ -0,0 +1,32 @@
+
+<section>
+ <title>Introduction</title>
+
+ <para>One of the most basic data structures which needs to be
+ represented in many bioinformatics applications is the biological
+ sequence. The sequence is a relatively simple data structure being
+ at heart an ordered sequence of elements, or in otherwords a
+ list, which is one of the "standard" data structures in computer
+ programming. </para>
+
+ <para>The Java language provides an relatively expensive API for
+ representing various data structures, known as the "Collections"
+ API. This includes several implementations of Lists. We decided
+ however that are several limitations to this representation for
+ use in the sequence API. <![%draft;[I need to discuss
+ this more in a later section]]> In this document we
+ dicuss the design and default implementation of an API which we
+ believe can form the basis for representing biological sequences
+ within applications using the Java language.</para>
+
+</section>
+
+
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
diff --git a/doc/sequence/requirements.sgml b/doc/sequence/requirements.sgml
new file mode 100644
index 0000000..edb93d8
--- /dev/null
+++ b/doc/sequence/requirements.sgml
@@ -0,0 +1,197 @@
+
+<section>
+ <title>Requirements for the &seqapi;.</title>
+
+ <para>In this section we discuss the basic requirements for the
+ &seqapi; both in terms of the data to be represented and the
+ requirements for any potential implementation. </para>
+
+ <section>
+ <title>The biological sequence as a list</title>
+
+ <para>As previously mentioned the biological sequence is in
+ essence a list, which is an ordered series of elements. The
+ basic operations that the Sequence should therefore provide
+ are:-
+
+ <itemizedlist>
+ <listitem>
+ <para>Access to the elements, in their appropriate
+ order.</para>
+ </listitem>
+ <listitem>
+ <para>Access to the size of the list</para>
+ </listitem>
+ <listitem>
+ <para>The ability to retrieve subsequences of the larger
+ sequence.</para>
+ </listitem>
+ </itemizedlist>
+ </para>
+
+ <![%draft;[
+ <para>
+ <emphasis>One thing that we have not really thought about with the
+ API at the moment is what notion of equality we have. The
+ obvious answer to this is to say that a sequence is equal
+ iff it all of its elements are equal and if the sequences
+ are of the same SequenceType. I am not sure though that this
+ is in fact the correct way to go. We also have a notion of
+ an identifier, and source, both of which should be also
+ considered. But how do we define the notion of equality of
+ these. I think perhaps equals and hashcode should be left as
+ they are and we should introduce and additional which checks
+ for "lexical" equality
+ </emphasis>
+ </para>
+ ]]>
+
+ </section>
+
+ <section>
+ <title>Modifying sequences</title>
+
+ <para>Many bioinformatics applications model sequences in
+ immutable data structures. This has several advantages. If a
+ sequence can not change it is not necesary to ensure that other
+ parts of the program are when changes happen to that
+ sequence. The Java language is also "multi-threaded", that
+ is it can do more than one thing at once. Multi-threaded programming
+ provides many advantages, but it's also inherantly
+ complex, as changes in one thread can affect another. Immutable
+ objects limit this complexity as the object can not be changed
+ in another thread. It is for this reason amoung others for
+ instance that the String class of Java is immutable.</para>
+
+ <para>Despite the appeal of immutable sequences and the
+ simplicity they provide they can also produce greater
+ complexity. If the application needs to alter sequences then
+ objects need to be re-created every time it is altered. As well
+ as being more complicated this can also have a large impact on
+ the computational performance of the class. We have decided that
+ despite the potential difficulties the &seqapi; should support
+ the ability to change sequences.</para>
+ </section>
+
+ <section>
+ <title>Conserving "type" information about
+ sequnces</title>
+
+ <para>There are many different types of biological sequences such
+ as protein, DNA and RNA sequences. When written down these
+ sequences are usually represented as a string of characters
+ (fortunately none of those mentioned have more that 26 different
+ elements!). One problem with this representation is that its not
+ possible to differentiate between a single letter, say a C
+ representing cytosine, or a cysteine. It doesn't normally make a
+ lot of sense to compare a protein sequence and a DNA sequence
+ directly. Additionally the requirement for mutable sequences
+ mean that it is potentially possible to add an amino acid to a
+ DNA sequence. This will almost always be a mistake.</para>
+
+ <para>Therefore we wanted the &seqapi; to build a degree of safety
+ into its operations, so that such errors could be easily
+ trapped, which should reduce the potential for bugs. This bears
+ a resemblance to the notion of type checking which is
+ implemented in Java, and indeed many other languages. Ideally we
+ would like the &seqapi; to exploit Java's type system, as this
+ would enable any such errors to be caught at compile
+ time. It should be noted however that Java's Collection's API,
+ which includes several implementations of Lists does not provide
+ this sort of type safety, which raises the suspision that it
+ might not be possible in the Java language. Therefore failing
+ compile time type safety the &seqapi; should "fail
+ fast", that is cause errors as soon as a possible type
+ error was detected, rather than continuing with potentially
+ corrupt data.</para>
+ </section>
+
+ <section>
+ <title>Representing more varied sequences: gaps, and complex
+ sequences</title>
+
+ <para>It is common in bioinformatics applications to align one
+ sequence with another, so that regions with the same or similar
+ sequences are placed next to each other. If sequences are
+ identical this is a trivial task, but this is not generally the
+ case, and it is frequently necessary to insert gaps into
+ sequences in order to align sequences. We required the abilty to
+ represent gapped sequences with the &seqapi;</para>
+
+ <para>As well as gapped sequences we wanted to be able to
+ represent sequences which are basically of one type, but which
+ have what can be considered to be modified residues. Examples of
+ this would be methylated cytosines in DNA, or phosphorylated
+ protein sequences. </para>
+ </section>
+
+ <section>
+ <title>Identifying the source of the sequence</title>
+
+ <para>In many cases the sequences being represented by the
+ &seqapi; will comes from a specific database. Sequence databases
+ usually come with an attached identifier for that sequence. This
+ API needs to be able to represent this data in a way which is
+ generic enough to cover most database formats.</para>
+ </section>
+
+ <section>
+ <title>Computation and programming requirements:- a lightweight
+ API</title>
+
+ <para>Perhaps because its one of the more basic data structures
+ found in computing science, there are many different
+ implementations of the list, all of which have different
+ implications of the CPU and memory usage. None of these
+ solutions are ideal, and the choice of which to use depends upon
+ the data being represented, and the application in question. The
+ &seqapi; should not require the use of one particular
+ implementation, but instead should allow easy replacements of
+ one implementation for another.</para>
+
+ <para>The primary purpose this API is to represent sequence
+ data. In order to be useful it should put as minimal a
+ requirement on the implementing programmer as is consistent with
+ its data task of representing the data. Where ever possible the
+ &seqapi; should provide default implementations and helper
+ classes to simplfy the implementation further. </para>
+
+ <para>Finally the API should reuse as many of the ideas, and
+ design patterns and classes of the core Java library as
+ possible. As well as not wishing to load the programmer down
+ with implementational requirements we want to ensure that the
+ API was as easy to understand as possible</para>
+
+ </section>
+
+ <section>
+ <title>Anti-requirements</title>
+
+ <para>In bioinformatics sequences are frequently associated with a
+ large body of associated information, in addition to the
+ sequences identifier, which can collectively be described as
+ sequence annotation. The &seqapi; specifically is not required
+ to represent this form of data. The reasoning behind this is
+ that firstly it contradicts the requirements for a simple,
+ lightweight API. Secondly sequence annotation is an extremely
+ complex issue, consisting as it does of a hetrogenous data
+ set. Whilst it would be good to have an API representing such
+ data it would far exceed the size of this API. Finally there is
+ nothing to preclude building up annotated sequence objects by
+ combining the objects in this API with objects representing the
+ state of the annotation.</para>
+ </section>
+</section>
+
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
+
+
+
+
diff --git a/doc/sequence/seqimpl.sgml b/doc/sequence/seqimpl.sgml
new file mode 100644
index 0000000..d421bf2
--- /dev/null
+++ b/doc/sequence/seqimpl.sgml
@@ -0,0 +1,315 @@
+
+<section>
+ <title>Sequence implementation</title>
+
+ <section>
+ <title>Overall design issues</title>
+
+ <para>One of the requirements for the &seqapi; is that it should
+ not require the use of a specific implementation of underlying
+ data structure. For that reason that API makes extensive use of
+ interfaces. All of the core classes are defined in the first
+ instance as a interface. These are extended with an abstact
+ class which implements many of the methods which can be defined
+ in terms of the other methods in the interface (so are not
+ implementation dependant) or alternatively where the default
+ implementation is held to be likely to be a good implementation
+ under most circumstances. Where ever possible we have used
+ object composition, to delegate functionality to external
+ classes. The support classes which provide this functionality
+ are also available within the API and can be re-used. We
+ have provided default implementations which fully implement the
+ interface. As far as possible these reuse standard classes
+ provided by the Java Collections API. </para>
+
+ </section>
+
+ <section>
+ <title>The implementation of sequence. </title>
+
+ <para>The sequence interface is relatively straight forward,
+ provided methods for accessing the elements, subsequences, and the
+ SequenceType.
+
+ <programlisting>
+
+ public interface Sequence extends Identifiable
+ {
+ public Sequence getSubSequence(int from, int length);
+ public char[] getSequenceAsChars();
+ public Element[] getSequenceAsElements();
+ public char getElementAtAsChar(int index);
+ public Element getElementAt(int index);
+ public SequenceType getSequenceType();
+ public int getLength();
+ }// Sequence
+
+ </programlisting>
+
+ We have provided the ability to access the sequence as char
+ arrays, because this allows easy printing. This has no impact on
+ the underlying implementation because the
+ <classname>Element</classname> interface provides a method for
+ obtaining a char representation of each
+ <classname>Element</classname>.</para>
+
+ <para>The default implementation of
+ <classname>Sequence</classname> called unsurprisingly
+ <classname>DefaultSequence</classname> implements this class using
+ a instance of <classname>java.util.ArrayList</classname>, which
+ is part of the Java Collections API. </para>
+
+ </section>
+
+ <section id="mutable">
+ <title id="mutable.title">Mutable Sequences</title>
+
+ <para>One of the requirements for the &seqapi; was that it should
+ be able to cope with sequences that change after they have been
+ created. Probably the most common method for doing this is for
+ the Sequence to signal events when ever it is changed, and to
+ allow other objects to listen for these events. </para>
+
+ <para>The biggest problem that an event system has for the
+ &seqapi; is that it could place a fairly large computational
+ load on using the sequences. The normal way to implement an
+ event system in Java, requires the creation of an Object for
+ each change that occurs, which could result in a large number of
+ events being called, and therefore a large number of Objects
+ created. It is for this reason combined with the desire not to
+ place additional load on the implementor of Sequence.</para>
+
+ <![%draft;[
+ <para>
+ <emphasis>One of the things that I do not like about this
+ arrangement is that if you have an object of type sequence you
+ can not know whether or not it is mutable, at least not
+ without doing an instanceof MutableSequence call. I suppose
+ that this is better than nothing but its a little bit
+ messy. As an alternative it would be possible to have defined
+ a "isMutable" method, and put the SequenceEventProducer
+ methods into the top level Sequence class. This is also a
+ little messy. The other problem is that it is perfectly
+ possible to implement a Sequence which can change, but which
+ does not have the listener methods. If the listener methods
+ were in the top level class then this would not be the case,
+ although it would always be possible to implement them
+ foolishly.</emphasis>
+ </para>
+ ]]>
+
+ <para>We have therefore defined the
+ <classname>MutableSequence</classname> class. This is the top
+ level class for Sequences which can change following
+ construction. As well as the <classname>Sequence</classname>
+ interface it extends the
+ <classname>SequenceEventProducer</classname> interface which
+ defines the following methods</para>
+
+ <programlisting>
+ public interface SequenceEventProvider
+ {
+ public void addSequenceListener(SequenceListener listener);
+
+ public void removeSequenceListener(SequenceListener listener);
+
+ public void addVetoableSequenceListener(VetoableSequenceListener listener);
+
+ public void removeVetoableSequenceListener(VetoableSequenceListener listener);
+
+ }// SequenceEventProvider
+ </programlisting>
+
+ <para>These methods provide the ability to add
+ <classname>SequenceListener's</classname> to give
+ <classname>Sequence</classname> instance. These listeners will
+ be informed when this <classname>Sequence</classname>
+ changes. Additionally there are methods for adding vetoable
+ Listeners, which throw an exception to prevent that
+ <classname>Sequence</classname> from changing. </para>
+
+ <para>Listeners are informed of the details of the
+ event via their only method</para>
+
+ <programlisting>
+ public interface SequenceListener extends EventListener
+ {
+ public void changeOccurred( SequenceEvent event );
+ }// SequenceListener
+ </programlisting>
+
+ <para>The <classname>SequenceEvent</classname> object carries with
+ it information about the region of the sequence affected by the
+ change and information about the type of change, if it is
+ known. We have provided this information because it can be used
+ to increase efficiency in some cases. Of course in many cases it
+ is just safer to assume that the entire Sequence has
+ changed.</para>
+
+ <para>It should be noted that MutableSequence itself does not
+ carry any methods for actually changing the underlying
+ sequence. This methods are provided for by the sub classes and
+ are described <link linkend="gappable.and.editable">next</link></para>
+ </section>
+
+ <section id="gappable.and.editable">
+ <title>Gapped and Editable Sequences</title>
+
+ <![%draft;[
+ <para><emphasis>Should this not really be
+ <classname>GappableSequence</classname>?</emphasis></para>
+ ]]>
+
+ <para>Aligning two sequences requires inserting gaps into one or
+ both of them. Gaps in sequences are supported by the
+ <classname>GappedSequence</classname>. This class provides a
+ series of methods which mirror those provided by
+ <classname>Sequence</classname> but instead return the
+ equivalent Gapped value. </para>
+
+ <programlisting>
+ public interface GappedSequence extends MutableSequence
+ {
+ public GappedSequence getGappedSubSequence( int from, int to );
+
+ public Element getGappedElementAt( int position );
+
+ public char getGappedElementAtAsChar( int position );
+
+ public Element[] getGappedSequenceAsElements();
+
+ public char[] getGappedSequenceAsChars();
+
+ public int getGappedLength();
+ [SNIP]
+ }
+ </programlisting>
+
+ <para>A call to the <function>getLength()</function> method of a
+ GappedSequence will therefore return the length of the sequence,
+ <emphasis>ignoring the gaps</emphasis>. The alternative method
+ <function>getGappedLength()</function> should be used to include
+ the gaps.</para>
+
+ <para>The reason that this approach was choosen was because the
+ <classname>Gap.GAP</classname> object will not be a part of the
+ SequenceType for a given sequence. For example, a gapped DNA
+ sequence can have one of five elements, namely A, C, G, T or a
+ Gap. Only the first four of these will be recognised as a member
+ of the <classname>DNASequenceType</classname>. It seems
+ inappropriate therefore that the
+ <function>getElementAt( int )</function>should
+ return <classname>Gap.GAP</classname>. This impacts all of the
+ other <classname>Sequence</classname> methods (with the
+ exception of <function>getSequenceType()</function>).</para>
+
+ <para>In order to support translation between the gapped and
+ ungapped length indexes there are two methods.
+
+ <programlisting>
+ public int getGappedPositionOf( int index );
+
+ public int getUngappedPositionOf( int index );
+ </programlisting>
+
+ For these methods
+ <function>getGappedPositionOf( getLength() )</function>,
+ should return <function>getGappedLength()</function>, whilst
+ <function>getUngappedPositionOf( getGappedLength() )</function>
+ should return <function>getLength()</function>.</para>
+
+ <para>The final methods required for a
+ <classname>GappedSequence</classname> are those to add and remove
+ Gaps from the sequence. These are as follows.
+
+ <programlisting>
+ public void insertGapAt( int index ) throws
+ NoSuchSequenceElementException, SequenceVetoException;
+
+ public void insertGapAt( int index, int length ) throws
+ NoSuchSequenceElementException, SequenceVetoException;
+
+ public void deleteGapAt( int index ) throws
+ NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException;
+
+ public void deleteGapAt( int index, int length ) throws
+ NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException;
+ </programlisting>
+ These methods take paramaters in terms of Gapped indexs. Changes
+ to the sequence caused by these methods will be signalled by the
+ event mechanism described in the section
+ <link linkend="mutable" endterm = "mutable.title"></link></para>
+
+ <para>The <classname>EditableSequence</classname> is designed in
+ a similar way, with methods for setting the
+ <classname>Element</classname>'s at a given index. These methods
+ are as follows</para>
+ <programlisting>
+ public interface EditableSequence extends MutableSequence
+ {
+ public Element setElementAt( Element element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public Element[] setElementAt( Element[] element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public void insertElementAt( Element element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public void insertElementAt( Element[] element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public Element deleteElementAt( int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public Element[] deleteElementAt( int index, int length )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+ }// EditableSequence
+ </programlisting>
+ <para>
+ As with the <classname>GappedSequence</classname> all of these
+ methods signal events and are Veto'able. Additionally these
+ methods are subject to a <classname>SequenceType</classname>
+ check, throwing an
+ <classname>InvalidSequenceTypeException</classname> if this
+ fails.
+ </para>
+ </section>
+
+ <section>
+ <title>Complex Sequences</title>
+
+ <para>The final class in the &seqapi; modelling Sequences is the
+ <classname>ComplexSequence</classname>. This is for modelling what
+ might be called "modififed" sequences. Examples of these
+ would include DNA sequences with methylated residues, or protein
+ sequences with any of the many post-translational
+ modifications. </para>
+
+ <para>This class is implemented in a similar way to the
+ <classname>GappedSequence</classname>. The standard
+ <classname>Sequence</classname> methods return
+ <classname>Element</classname>'s which unmodified, and will be
+ identified as part of the
+ <classname>SequenceType</classname>. </para>
+
+ <para>It would probably be a good idea to actually write
+ this. </para>
+ </section>
+</section>
+
+
+<!--
+ We need to define local variables to enable psgml mode to work out
+ what DTD we are using, and also where we are in the document.
+
+ Local Variables: ***
+ sgml-parent-document:("sequence.sgml" "article" "section" ) ***
+ End: ***
+ -->
+
+
+
+
+
+
diff --git a/doc/sequence/sequence.sgml b/doc/sequence/sequence.sgml
new file mode 100644
index 0000000..a6268a1
--- /dev/null
+++ b/doc/sequence/sequence.sgml
@@ -0,0 +1,74 @@
+<!DOCTYPE article PUBLIC "-//OASIS//DTD DocBook V3.1//EN" [
+<!ENTITY intro SYSTEM "intro.sgml">
+<!ENTITY requirements SYSTEM "requirements.sgml">
+<!ENTITY elementandtype SYSTEM "elementandtype.sgml">
+<!ENTITY seqimpl SYSTEM "seqimpl.sgml">
+<!ENTITY alignment SYSTEM "alignment.sgml">
+<!ENTITY conclusions SYSTEM "conclusions.sgml">
+<!ENTITY seqapi "Sequence API for Java">
+<!ENTITY % draft "INCLUDE">
+]>
+
+
+<article>
+ <title>An API for describing biological sequences written in the
+ Java language</title>
+ <artheader>
+ <author>
+ <honorific>Dr</honorific>
+ <firstname>Phillip</firstname>
+ <surname>Lord</surname>
+ <affiliation>
+ <orgname>The University of Manchester</orgname>
+ <orgdiv>Department of Biological Sciences</orgdiv>
+ <address>
+ <otheraddr>2.18, Stopford Buildings</otheraddr>
+ <street>Oxford Road</street>
+ <city>Manchester</city>
+ <postcode>M13 9PT</postcode>
+ </address>
+ </affiliation>
+ </author>
+ <pubdate>$Revision: 1.1 $, $Date: 2000/11/22 16:27:00 $</pubdate>
+ </artheader>
+
+ <abstract>
+ <title>Abstract</title>
+
+ <para>This document contains a description of the design and
+ implementation of the &seqapi;. It is a series of Java classes
+ and interfaces which can be used to enable the representation
+ and manipulation of biological sequences in the Java
+ language. The API has been designed to be as lightweight as
+ possible, whilst still allowing considerable
+ flexibility. </para>
+ <![%draft;[
+ <para>
+ <emphasis>This documentation is a work in progress at the
+ moment. And although the &seqapi; is much more stable it is
+ still changing occasionally. Please bear this in mind when you
+ read it. </emphasis>
+ </para>
+ ]]>
+ </abstract>
+
+ <!-- The introduction -->
+ &intro;
+ <!-- The requirements -->
+ &requirements;
+ <!-- The implementation of elements and types-->
+ &elementandtype;
+ <!-- And of sequences themselves-->
+ &seqimpl;
+ <!-- Sequence Alignments -->
+ &alignment;
+ <!-- Conclusions -->
+ &conclusions;
+</article>
+
+
+
+
+
+
+
diff --git a/lib/app_support.jar b/lib/app_support.jar
new file mode 100644
index 0000000..aa418c8
Binary files /dev/null and b/lib/app_support.jar differ
diff --git a/lib/cinema.jar b/lib/cinema.jar
new file mode 100644
index 0000000..3adb5a5
Binary files /dev/null and b/lib/cinema.jar differ
diff --git a/lib/emboss.jar b/lib/emboss.jar
new file mode 100644
index 0000000..15cb0ec
Binary files /dev/null and b/lib/emboss.jar differ
diff --git a/lib/ext/gnu-getopt.jar b/lib/ext/gnu-getopt.jar
new file mode 100644
index 0000000..9bd4595
Binary files /dev/null and b/lib/ext/gnu-getopt.jar differ
diff --git a/lib/ext/jakarta-regexp.jar b/lib/ext/jakarta-regexp.jar
new file mode 100644
index 0000000..713441c
Binary files /dev/null and b/lib/ext/jakarta-regexp.jar differ
diff --git a/lib/ext/xerces.jar b/lib/ext/xerces.jar
new file mode 100644
index 0000000..3b5659c
Binary files /dev/null and b/lib/ext/xerces.jar differ
diff --git a/lib/graph.jar b/lib/graph.jar
new file mode 100644
index 0000000..15cb0ec
Binary files /dev/null and b/lib/graph.jar differ
diff --git a/lib/gui.jar b/lib/gui.jar
new file mode 100644
index 0000000..18d3ef3
Binary files /dev/null and b/lib/gui.jar differ
diff --git a/lib/mxc.jar b/lib/mxc.jar
new file mode 100644
index 0000000..bbfee9d
Binary files /dev/null and b/lib/mxc.jar differ
diff --git a/lib/sequence.jar b/lib/sequence.jar
new file mode 100644
index 0000000..ad05ff7
Binary files /dev/null and b/lib/sequence.jar differ
diff --git a/lib/src.jar b/lib/src.jar
new file mode 100644
index 0000000..0d4a94d
Binary files /dev/null and b/lib/src.jar differ
diff --git a/lib/util.jar b/lib/util.jar
new file mode 100644
index 0000000..7a45509
Binary files /dev/null and b/lib/util.jar differ
diff --git a/src/uk/ac/man/bioinf/Y.java b/src/uk/ac/man/bioinf/Y.java
new file mode 100644
index 0000000..27694dd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/Y.java
@@ -0,0 +1,47 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf; // Package name inserted by JPack
+
+
+/**
+ * Y.java
+ *
+ * Class created entirely for the purpose of being tab
+ * completable. Originally I used X.java, which is not buzz word
+ * compliant, as I have forgotten about XML. Idiot!
+ *
+ * Created: Mon May 8 21:24:52 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Y.java,v 1.1 2000/05/15 16:19:46 lord Exp $
+ */
+
+public class Y
+{
+
+ public Y()
+ {
+
+ }
+
+} // Y
+
+
+
+/*
+ * ChangeLog
+ * $Log: Y.java,v $
+ * Revision 1.1 2000/05/15 16:19:46 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.java b/src/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.java
new file mode 100644
index 0000000..da14660
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/consensus/ConsensusCalculator.java
@@ -0,0 +1,78 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+/**
+ * ConsensusCalculator.java
+ *
+ *
+ * Created: Thu Jun 15 15:11:33 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ConsensusCalculator.java,v 1.6 2001/04/11 17:04:41 lord Exp $
+ */
+
+public interface ConsensusCalculator
+{
+ public SequenceAlignment getSequenceAlignment();
+
+ public GappedSequence getCurrentConsensus();
+
+ public String getCalculatorName();
+
+}// ConsensusCalculator
+
+
+/*
+ * ChangeLog
+ * $Log: ConsensusCalculator.java,v $
+ * Revision 1.6 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/12/05 15:08:52 lord
+ * Import rationalisation
+ *
+ * Revision 1.4 2000/11/08 18:24:47 lord
+ * The consensus calculator interface has been changed to reflect the
+ * fact that instances are expected to have state, that is to be tied to
+ * a specific SequenceAlignment
+ *
+ * Revision 1.3 2000/10/19 17:33:49 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/08/01 16:05:50 lord
+ * Instance now tied to a specific SequenceAlignment
+ *
+ * Revision 1.1 2000/06/27 15:53:56 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.java b/src/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.java
new file mode 100644
index 0000000..13aa100
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/consensus/ConsensusIdentifier.java
@@ -0,0 +1,81 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier;
+import uk.ac.man.bioinf.sequence.identifier.NoSource;
+import uk.ac.man.bioinf.sequence.identifier.Source;
+
+
+/**
+ * ConsensusIdentifier.java
+ *
+ *
+ * Created: Mon Oct 16 15:40:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ConsensusIdentifier.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class ConsensusIdentifier extends AbstractIdentifier
+{
+ private String title;
+
+ public ConsensusIdentifier( SequenceAlignment alignment )
+ {
+ this( new NoSource(), alignment );
+ }
+
+ public ConsensusIdentifier( Source source, SequenceAlignment alignment )
+ {
+ super( source );
+ this.title = "Consensus: " + alignment.getIdentifier().getTitle();
+ }
+
+ public String getTitle()
+ {
+ return title;
+ }
+} // ConsensusIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: ConsensusIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/10 15:11:10 lord
+ * Added imports
+ *
+ * Revision 1.1 2000/10/19 17:34:32 lord
+ * Consensus sequences now have an sane "getTitle()" identifier method
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.java b/src/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.java
new file mode 100644
index 0000000..40f83b8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/consensus/ConsensusSequence.java
@@ -0,0 +1,70 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+/**
+ * ConsensusSequence.java
+ *
+ *
+ * Created: Thu Jun 15 15:32:13 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ConsensusSequence.java,v 1.4 2001/04/11 17:04:41 lord Exp $
+ */
+
+public interface ConsensusSequence extends GappedSequence
+{
+ public void setConsensusCalculator( ConsensusCalculator calc );
+
+ public ConsensusCalculator getConsensusCalculator();
+
+ public void destroy();
+
+}// ConsensusSequence
+
+
+/*
+ * ChangeLog
+ * $Log: ConsensusSequence.java,v $
+ * Revision 1.4 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/11/08 18:25:36 lord
+ * As calculator has state no longer stores reference to Alignment.
+ * Added destroy method to stop calculation going on.
+ *
+ * Revision 1.1 2000/06/27 15:53:56 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.java b/src/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.java
new file mode 100644
index 0000000..35e3581
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/consensus/DefaultConsensusSequence.java
@@ -0,0 +1,244 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.EmptyGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceEventType;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * DefaultConsensusSequence.java
+ *
+ *
+ * Created: Thu Jun 15 17:00:04 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultConsensusSequence.java,v 1.8 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class DefaultConsensusSequence extends AbstractGappedSequence
+ implements ConsensusSequence, AlignmentListener, SequenceListener
+{
+ private GappedSequence currentConsensus = EmptyGappedSequence.getInstance();
+ private ConsensusCalculator calculator;
+ private VetoableSequenceListener seqListener;
+
+ public DefaultConsensusSequence( ConsensusCalculator calculator )
+ {
+ super( calculator.getSequenceAlignment().getSequenceType() );
+ // this constructor is actually fairly tricky as you have to get
+ // things in the right order or it all falls down.
+ this.calculator = calculator;
+ installAlignmentListeners( calculator );
+ installVetoListeners();
+ validate();
+ }
+
+ protected void installVetoListeners()
+ {
+ addVetoableSequenceListener
+ ( seqListener = new VetoableSequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ }
+
+ public void vetoableChangeOccurred( VetoableSequenceEvent event ) throws SequenceVetoException
+ {
+ throw new SequenceVetoException( "Consensus sequences can't be changed except by themselves", event );
+ }
+ });
+ }
+
+ protected void installAlignmentListeners( ConsensusCalculator cons )
+ {
+ cons.getSequenceAlignment().addSequenceListener ( this );
+ cons.getSequenceAlignment().addAlignmentListener( this );
+ }
+
+ protected void uninstallAlignmentListners( ConsensusCalculator cons )
+ {
+ cons.getSequenceAlignment().removeSequenceListener ( this );
+ cons.getSequenceAlignment().removeAlignmentListener( this );
+ }
+
+ protected void validate()
+ {
+ calcConsensus();
+ fireChangeEvent();
+ }
+
+ protected void fireChangeEvent()
+ {
+ fireSequenceEvent( new SequenceEvent( this, 1, getGappedLength(), SequenceEventType.UNSPECIFIED ) );
+ }
+
+ protected void calcConsensus()
+ {
+ currentConsensus.removeVetoableSequenceListener( seqListener );
+ currentConsensus = calculator.getCurrentConsensus();
+ currentConsensus.addVetoableSequenceListener( seqListener );
+ }
+
+ // listener methods
+ public void changeOccurred( SequenceEvent event )
+ {
+ validate();
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ validate();
+ }
+
+ // delegation methods
+ public Element getElementAt( int index )
+ {
+ return currentConsensus.getElementAt( index );
+ }
+
+
+ public Element getGappedElementAt( int index )
+ {
+ return currentConsensus.getGappedElementAt( index );
+ }
+
+ public int getGappedLength()
+ {
+ return currentConsensus.getGappedLength();
+ }
+
+ public int getGappedPositionOf( int index )
+ {
+ return currentConsensus.getGappedPositionOf( index );
+ }
+
+ public Element[] getGappedSequenceAsElements()
+ {
+ return currentConsensus.getGappedSequenceAsElements();
+ }
+
+ public GappedSequence getGappedSubSequence( int start, int length )
+ {
+ return currentConsensus.getGappedSubSequence( start, length );
+ }
+
+ public int getUngappedPositionOf( int index )
+ {
+ return currentConsensus.getUngappedPositionOf( index );
+ }
+
+ public int getLength()
+ {
+ return currentConsensus.getLength();
+ }
+
+ public Element[] getSequenceAsElements()
+ {
+ return currentConsensus.getSequenceAsElements();
+ }
+
+ public Identifier getIdentifier()
+ {
+ return currentConsensus.getIdentifier();
+ }
+
+ public void setConsensusCalculator( ConsensusCalculator calculator )
+ {
+ this.calculator = calculator;
+ validate();
+ }
+
+ public ConsensusCalculator getConsensusCalculator()
+ {
+ return calculator;
+ }
+
+ // gap element methods which should all fire veto's
+ public void deleteGapAtQuietly( int index )
+ {
+ }
+
+ public void insertGapAtQuietly( int index )
+ {
+ }
+
+ public void destroy()
+ {
+ uninstallAlignmentListners( calculator );
+ // we are no longer listening to the alignment so therefore we
+ // want to null the calculator to allow GC, and set the current
+ // consensus to empty to prevent using an out of date sequence.
+ calculator = null;
+ currentConsensus = EmptyGappedSequence.getInstance();
+ }
+} // DefaultConsensusSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultConsensusSequence.java,v $
+ * Revision 1.8 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.6 2000/12/05 15:09:06 lord
+ * Removed debug statement
+ *
+ * Revision 1.5 2000/11/08 18:26:33 lord
+ * Major rewiring. Split quite a few methods to allow subclass
+ * over-riding. ConsensusCalculator now has state so changes made to
+ * reflect this.
+ *
+ * Revision 1.4 2000/09/11 14:00:13 lord
+ * SequenceIdentifier renamed to Identifier
+ *
+ * Revision 1.3 2000/08/01 16:06:21 lord
+ * Instance now tied to a specific SequenceAlignment
+ *
+ * Revision 1.2 2000/07/18 10:35:10 lord
+ * Removed biointerface, and replaced it with identifiable
+ *
+ * Revision 1.1 2000/06/27 15:53:56 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.java b/src/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.java
new file mode 100644
index 0000000..05b8104
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/consensus/PercentageIDConsensus.java
@@ -0,0 +1,129 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusIdentifier;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * PercentageIDConsensus.java
+ *
+ * Calculates a consensus sequence based simply on which element is
+ * most frequent at that row. If there are several possibilities it
+ * just takes which ever one came first.
+ *
+ * Created: Thu Jun 15 18:06:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: PercentageIDConsensus.java,v 1.10 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class PercentageIDConsensus implements ConsensusCalculator
+{
+ public static final String NAME = "Percentage ID Consensus Calculator";
+
+ private PercentageIDCalculator calc;
+ private GappedSequence sequence;
+ private int checksum = -1;
+
+ public PercentageIDConsensus( PercentageIDCalculator calc )
+ {
+ this.calc = calc;
+ }
+
+ private void fetchConsensus()
+ {
+ sequence = Sequences.
+ getElementsAsGappedSequence( calc.getConsensus(),
+ calc.getAlignment().getSequenceType(),
+ new ConsensusIdentifier( calc.getAlignment() ) );
+ checksum = calc.getCheckSum();
+ }
+
+ public GappedSequence getCurrentConsensus()
+ {
+ if( checksum != calc.getCheckSum() ){
+ fetchConsensus();
+ }
+ return sequence;
+ }
+
+ public String getCalculatorName()
+ {
+ return NAME;
+ }
+
+ public SequenceAlignment getSequenceAlignment()
+ {
+ return calc.getAlignment();
+ }
+} // PercentageIDConsensus
+
+
+
+/*
+ * ChangeLog
+ * $Log: PercentageIDConsensus.java,v $
+ * Revision 1.10 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.9 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.8 2000/11/13 16:52:11 jns
+ * o bug fixing because a class has moved else where in the tree
+ *
+ * Revision 1.7 2000/11/08 18:26:57 lord
+ * Calculator now has state
+ *
+ * Revision 1.6 2000/10/19 17:34:32 lord
+ * Consensus sequences now have an sane "getTitle()" identifier method
+ *
+ * Revision 1.5 2000/08/01 16:07:06 lord
+ * PercentageIDCalculator is now tied to a specific SequenceAlignment
+ * instance.
+ * The name of this Calculator is now available as a public static final string
+ *
+ * Revision 1.4 2000/07/26 13:24:56 lord
+ * Last comment is wrong. I have changed this in response to changes
+ * in PercentageIDCalculator which is now tied to a specific alignment
+ *
+ * Revision 1.3 2000/07/26 13:23:26 lord
+ * Have now tied Object instance to specific SequenceAlignment
+ *
+ * Revision 1.2 2000/07/18 10:35:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/06/27 15:53:56 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.java b/src/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.java
new file mode 100644
index 0000000..4673c2e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/consensus/ThreadedConsensusSequence.java
@@ -0,0 +1,129 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.invoker.AnonInvoker;
+import uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue;
+
+
+/**
+ * ThreadedConsensusSequence.java
+ *
+ * This class calls the calculation out of the event thread, so that
+ * background analysis is made more easily. To use this class you have
+ * to provide it with a thread that it can use for the
+ * calculation. You can do this either on a per instance basis, or by
+ * setting a static default. You have to do one of the other though!
+ *
+ * Created: Tue Nov 7 18:36:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ThreadedConsensusSequence.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class ThreadedConsensusSequence extends DefaultConsensusSequence
+{
+
+ private InvokerInternalQueue queue;
+
+ public ThreadedConsensusSequence( ConsensusCalculator calculator )
+ {
+ this( calculator, getDefaultInvokerInternalQueue() );
+ if( queue == null )
+ throw new NullPointerException( "You have to either set a default queue, or provide on in the constructor" );
+ }
+
+ public ThreadedConsensusSequence( ConsensusCalculator calculator, InvokerInternalQueue queue )
+ {
+ super( calculator );
+ this.queue = queue;
+ }
+
+ protected void validate()
+ {
+ // we want to do the calculation out of the event thread, and then
+ // fire change events back in it...
+ if( queue != null ){
+ queue.makeEmpty();
+ queue.enqueue
+ ( new AnonInvoker(){
+ public Object slow()
+ {
+ ThreadedConsensusSequence.this.calcConsensus();
+ return null;
+ }
+
+ public void doRun()
+ {
+ ThreadedConsensusSequence.this.
+ fireChangeEvent();
+ }
+ });
+ }
+ else{
+ // the first time around we want to super class validate.
+ super.validate();
+ }
+ }
+
+ public void destroy()
+ {
+ super.destroy();
+ // the queue has to be shut down manually because it is a system
+ // event listener and this will prevent it from GC otherwise.
+ queue.destroy();
+ }
+
+ private static InvokerInternalQueue qu;
+
+ public static void setDefaultInvokerInternalQueue( InvokerInternalQueue queue )
+ {
+ qu = queue;
+ }
+
+ public static InvokerInternalQueue getDefaultInvokerInternalQueue()
+ {
+ return qu;
+ }
+} // ThreadedConsensusSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: ThreadedConsensusSequence.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:09:23 lord
+ * Added proper destroy method.
+ *
+ * Revision 1.1 2000/11/08 18:27:38 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.java b/src/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.java
new file mode 100644
index 0000000..8ecbdca
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculator.java
@@ -0,0 +1,206 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.misc; // Package name inserted by JPack
+
+
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.alignment.AlignmentColumn;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.util.ChangeableListenerSupport;
+
+
+/**
+ * PercentageIDCalculator.java
+ *
+ * This class performs a variance calculation on the given sequence
+ * alignment. The calculation is done by calling the
+ * calculateAlignment method, and the results got from the
+ * getVariance, and getConsensus methods. Both calculations are done
+ * by a simple Percentage ID calculation.
+ *
+ * Created: Fri Jun 16 18:38:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: PercentageIDCalculator.java,v 1.6 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class PercentageIDCalculator implements AlignmentListener, SequenceListener
+{
+ private AlignmentColumn col = new AlignmentColumn();
+ private double[] variance;
+ private Element[] consensus;
+ private SequenceAlignment alignment;
+ private ChangeableListenerSupport supp = new ChangeableListenerSupport();
+ private boolean invalid = true;
+ private int checksum = 0;
+
+ public PercentageIDCalculator( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ alignment.addAlignmentListener( this );
+ alignment.addSequenceListener( this );
+ }
+
+ private synchronized void calculate()
+ {
+ // we need the sequence type to before several operations for us.
+ SequenceType type = alignment.getSequenceType();
+
+ // start new arrays to store the results.
+ consensus = new Element[ alignment.getLength() ];
+ variance = new double[ alignment.getLength() ];
+
+ // this hash is used to store the number of an element in a
+ // column.
+ int[] hash = new int[ type.size() ];
+ col.setAlignment( alignment );
+
+ int lastColumn = alignment.getLength() + 1;
+ int lastRow = alignment.getNumberSequences() + 1;
+
+ // iterate through all of the columns
+ for( int i = 1; i < lastColumn; i++ ){
+ int gapElements = 0;
+ col.setColumn( i );
+
+ // count up the number of a specific element type.
+ for( int j = 1; j < lastRow; j++ ){
+ Element elementAtRow = col.getElementAtRow( j );
+
+ if( elementAtRow != Gap.GAP ){
+ hash[ type.getIntForElement( elementAtRow ) ]++;
+ }
+ else{
+ gapElements++;
+ }
+ }
+
+ int largestValue = 0;
+ for( int j = 0; j < hash.length; j++ ){
+ // find how many times the most frequently occuring element
+ // occurs
+ if( hash[ j ] > largestValue ){
+ largestValue = hash[ j ];
+ consensus[ i - 1 ] = type.getElementForInt( j );
+ }
+
+ // zero this for the next time around.
+ hash[ j ] = 0;
+
+ // check that gaps did not occur more frequently.
+ if( gapElements > largestValue ){
+ consensus[ i - 1 ] = Gap.GAP;
+ }
+ }
+
+ // dont want to divide by zero
+ if( lastRow != 1 ){
+ // calculate the variance at this row.
+ variance[ i - 1 ] = ((double)largestValue) / ((double)(lastRow - 1) );
+ }
+ }
+ invalid = false;
+ }
+
+ private void invalidate()
+ {
+ checksum++;
+ invalid = true;
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ invalidate();
+ }
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ invalidate();
+ }
+
+ /**
+ * Returns a checksum value. If this value has changed there
+ * consensus sequence may well have changed.
+ * @return a value of type 'int'
+ */
+ public synchronized int getCheckSum()
+ {
+ return checksum;
+ }
+
+ public synchronized double[] getVariance()
+ {
+ if( invalid ) calculate();
+
+ return variance;
+ }
+
+ public synchronized Element[] getConsensus()
+ {
+ if( invalid ) calculate();
+
+ return consensus;
+ }
+
+ public SequenceAlignment getAlignment()
+ {
+ return alignment;
+ }
+} // PercentageIDCalculator
+
+
+
+/*
+ * ChangeLog
+ * $Log: PercentageIDCalculator.java,v $
+ * Revision 1.6 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/31 17:39:33 lord
+ * Spelling correction
+ *
+ * Revision 1.4 2000/11/10 15:11:28 lord
+ * Removed some imports
+ *
+ * Revision 1.3 2000/11/08 18:28:54 lord
+ * Lots of changes. Object now has state. Added checksum, added listeners.
+ *
+ * Revision 1.2 2000/07/26 13:25:44 lord
+ * Now implements Changeable, and it tied to a specific SequenceAlignment instance
+ *
+ * Revision 1.1 2000/06/27 15:53:56 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.java b/src/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.java
new file mode 100644
index 0000000..e96f7ef
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/misc/PercentageIDCalculatorManager.java
@@ -0,0 +1,84 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.misc; // Package name inserted by JPack
+import java.util.WeakHashMap;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * PercentageIDCalculatorManager.java
+ *
+ *
+ * Created: Tue Nov 7 17:59:02 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: PercentageIDCalculatorManager.java,v 1.2 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class PercentageIDCalculatorManager
+{
+ private WeakHashMap weakHash;
+
+ public PercentageIDCalculatorManager()
+ {
+ weakHash = new WeakHashMap();
+ }
+
+ public PercentageIDCalculator getCalculator( SequenceAlignment alignment )
+ {
+ // have we cached a calculator for this alignment
+ PercentageIDCalculator calc = (PercentageIDCalculator)weakHash.get( alignment );
+
+ if( calc == null ){
+ calc = new PercentageIDCalculator( alignment );
+ }
+ return calc;
+ }
+
+ private static PercentageIDCalculatorManager instance;
+ public static PercentageIDCalculatorManager getDefaultInstance()
+ {
+ if( instance == null ) instance = new PercentageIDCalculatorManager();
+ return instance;
+ }
+} // PercentageIDCalculatorManager
+
+
+
+/*
+ * ChangeLog
+ * $Log: PercentageIDCalculatorManager.java,v $
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/08 18:29:47 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.java b/src/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.java
new file mode 100644
index 0000000..e531d0b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/regexp/GappedSequenceCharacterIterator.java
@@ -0,0 +1,87 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.regexp; // Package name inserted by JPack
+import org.apache.regexp.CharacterIterator;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.Sequences;
+
+
+/**
+ * GappedSequenceCharacterIterator.java
+ *
+ *
+ * Created: Mon Feb 5 14:06:28 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: GappedSequenceCharacterIterator.java,v 1.2 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class GappedSequenceCharacterIterator implements CharacterIterator
+{
+ private GappedSequence seq;
+
+ public GappedSequenceCharacterIterator( GappedSequence seq )
+ {
+ this.seq = seq;
+ }
+
+ public char charAt( int at )
+ {
+ //System.out.print( at + " " + seq.getGappedElementAtAsChar( at + 1 ) + ": " );
+ return seq.getGappedElementAtAsChar( at + 1 );
+ }
+
+ public boolean isEnd( int position )
+ {
+ return ((position + 1) >= seq.getLength() );
+ }
+
+ public String substring( int index )
+ {
+ return Sequences.getGappedSubSequenceAsString( seq, (index + 1), seq.getGappedLength() );
+ }
+
+ public String substring( int index, int length )
+ {
+ return Sequences.getGappedSubSequenceAsString( seq, (index + 1), length );
+ }
+} // GappedSequenceCharacterIterator
+
+
+
+/*
+ * ChangeLog
+ * $Log: GappedSequenceCharacterIterator.java,v $
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 16:47:55 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.java b/src/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.java
new file mode 100644
index 0000000..1775ad2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/analysis/regexp/SequenceCharacterIterator.java
@@ -0,0 +1,90 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.analysis.regexp; // Package name inserted by JPack
+import org.apache.regexp.CharacterIterator;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.Sequences;
+
+
+/**
+ * SequenceCharacterIterator.java
+ *
+ * This class provides the link between the sequence package and
+ * jakarta regexp package. This class can be used as a wrapper for
+ * Sequences.
+ * @see GappedSequenceCharacterIterator
+ *
+ * Created: Mon Feb 5 13:53:45 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceCharacterIterator.java,v 1.2 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class SequenceCharacterIterator implements CharacterIterator
+{
+ private Sequence seq;
+
+ public SequenceCharacterIterator( Sequence seq )
+ {
+ this.seq = seq;
+ }
+
+ public char charAt( int at )
+ {
+ return seq.getElementAtAsChar( at + 1 );
+ }
+
+ public boolean isEnd( int position )
+ {
+ return ((position + 1) >= seq.getLength() );
+ }
+
+ public String substring( int index )
+ {
+ return Sequences.getSubSequenceAsString( seq, (index + 1), seq.getLength() );
+ }
+
+ public String substring( int index, int length )
+ {
+ return Sequences.getSubSequenceAsString( seq, (index + 1), length );
+ }
+} // SequenceCharacterIterator
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceCharacterIterator.java,v $
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 16:47:55 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/Cinema.java b/src/uk/ac/man/bioinf/apps/cinema/Cinema.java
new file mode 100644
index 0000000..b34e242
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/Cinema.java
@@ -0,0 +1,180 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import java.io.File;
+import java.io.IOException;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleFactoryInstance;
+import uk.ac.man.bioinf.module.ModuleIdentifier;
+
+
+/**
+ * Cinema.java
+ *
+ *
+ * Created: Fri May 26 22:04:20 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Cinema.java,v 1.15 2001/05/04 12:30:32 lord Exp $
+ */
+
+public class Cinema
+{
+ private static ModuleFactoryInstance moduleFactory;
+ private static String[] cmdLnArgs; // stores the command line
+ // arguments supplied to Cinema
+
+ public static void main( String[] args )
+ {
+ try{
+ cmdLnArgs = args; // store the arguments
+ moduleFactory = createModuleFactoryInstance();
+ moduleFactory.load( CinemaBootIdentifier.CINEMA_SHARED );
+
+
+ startCinemaInstance();
+ }
+ catch( Throwable t ){
+ if( Debug.debug )
+ Debug.both( Cinema.class, "Cinema Panic!", t );
+ System.out.println( "Cinema Panic! Error in loading Core Cinema Modules!" );
+ System.out.println( "Giving Up! Sorry!" );
+ t.printStackTrace();
+ System.exit( -1 );
+ }
+ } //end main method
+
+ /**
+ * Returns the arguments supplied to Cinema on the command line, and
+ * stored in the 'main' function.
+ * @return the arguments
+ */
+ public static String[] getCommandLineArguments()
+ {
+ return cmdLnArgs;
+ }
+
+ public static Module getSharedModuleInstance( ModuleIdentifier identifier )
+ throws ModuleException
+ {
+ return moduleFactory.getModule( identifier );
+ }
+
+ public static ModuleFactoryInstance startCinemaInstance() throws ModuleException
+ {
+ // Set up the factory
+ return startCinemaInstance( createModuleFactoryInstance() );
+ }
+
+ private static ModuleFactoryInstance createModuleFactoryInstance()
+ {
+ ModuleFactoryInstance moduleFactoryInstance = new CinemaModuleFactoryInstance();
+ moduleFactoryInstance.addIdentifier
+ ( AbstractEnumeratedModuleIdentifier.getAllIdentifiers( CinemaBootIdentifier.class ) );
+ return moduleFactoryInstance;
+ }
+
+ private static ModuleFactoryInstance startCinemaInstance
+ ( ModuleFactoryInstance moduleFactory ) throws ModuleException
+ {
+ // load the core identifiers
+ moduleFactory.
+ addIdentifier( AbstractEnumeratedModuleIdentifier.getAllIdentifiers
+ ( CinemaModuleCoreIdentifier.class ) );
+
+ // load the XMLBoot Module which will load everything else
+ moduleFactory.load( CinemaBootIdentifier.CINEMA_BOOT );
+ return moduleFactory;
+ }
+} // Cinema
+
+
+
+/*
+ * ChangeLog
+ * $Log: Cinema.java,v $
+ * Revision 1.15 2001/05/04 12:30:32 lord
+ * Cosmetic changes
+ *
+ * Revision 1.14 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.13 2001/02/19 16:49:01 lord
+ * Removed all the classpath stuff again
+ *
+ * Revision 1.12 2001/02/15 18:59:12 lord
+ * Actually calls construct class path now.
+ *
+ * Revision 1.11 2001/02/15 18:50:42 lord
+ * bug fix
+ *
+ * Revision 1.10 2001/02/15 18:20:48 lord
+ * Support for automatic classpath insertion
+ *
+ * Revision 1.9 2001/01/31 17:40:27 lord
+ * Exception handling change
+ *
+ * Revision 1.8 2001/01/04 14:50:50 lord
+ * startCinemaInstance now returns the module factory. This allows the
+ * class which is starting a new CinemaInstance to interact with the new
+ * instance. The motivation for this was to allow setting the
+ * SequenceAlignment of the new instance.
+ *
+ * Revision 1.7 2001/01/04 12:57:30 jns
+ * o CINEMA command line processor. Code will be improved to look at an
+ * XML file and from there load relevent code. Currently the code simply
+ * loads a file from the command line, and has the option for a parser to
+ * be specified. -i <filename> or <filename> to simply load a file. The
+ * PIR parser is currently used by default (there are no other parsers as
+ * yet).
+ *
+ * Revision 1.6 2000/12/13 19:35:03 lord
+ * Cinema now shuts down if a Cinema Panic occurs
+ *
+ * Revision 1.5 2000/09/15 17:26:26 lord
+ * Changed boot sequence to include support for multiple cinema instances
+ *
+ * Revision 1.4 2000/08/02 14:54:20 lord
+ * Removed test status bar message
+ *
+ * Revision 1.3 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.2 2000/06/27 13:36:37 lord
+ * Added stack trace to exception handling
+ *
+ * Revision 1.1 2000/05/30 16:05:54 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaBoot.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaBoot.java
new file mode 100644
index 0000000..6925e98
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaBoot.java
@@ -0,0 +1,130 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import java.io.IOException;
+import java.io.InputStream;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXParseException;
+import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
+import uk.ac.man.bioinf.apps.xml.XMLBootModule;
+import uk.ac.man.bioinf.module.ModuleException;
+
+
+/**
+ * CinemaBoot.java
+ *
+ *
+ * Created: Mon May 29 17:58:12 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaBoot.java,v 1.8 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaBoot extends XMLBootModule
+{
+ public void load() throws ModuleException
+ {
+ try{
+ super.load();
+ }
+ catch( ModuleException me ){
+ System.out.println( "Exception in Cinema Boot" );
+ System.out.println( me );
+ me.printStackTrace();
+
+ Throwable thrw = me.getThrowable();
+
+ // we need to test for a SAXException, as this will have
+ // swallowed the original exception resulting in a useless
+ // stack trace.
+ if( thrw instanceof SAXParseException ){
+ System.out.println( "Problem parsing config files: " + thrw.getMessage() );
+ SAXParseException spe = (SAXParseException)thrw;
+ System.out.println( "In " + spe.getSystemId() + " at " + spe.getLineNumber() + ":" + spe.getColumnNumber() );
+ }
+ else{
+ me.getThrowable().printStackTrace();
+ }
+ throw me;
+ }
+ }
+
+ public String fetchMainBootName()
+ {
+ return "cinema-main.xml";
+ }
+
+ public String fetchModuleSystemIdentifier()
+ {
+ return CinemaResources.fetchModuleSystemIdentifier();
+ }
+
+ public InputStream resolveXMLLoadName( String loadName ) throws IOException
+ {
+ return CinemaResources.resolveXMLLoadName( loadName );
+ }
+
+ protected String getXMLParserClass()
+ {
+ return CinemaXMLParserFactory.class.getName();
+ }
+} // CinemaBoot
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaBoot.java,v $
+ * Revision 1.8 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2001/01/26 17:08:04 lord
+ * Improved exception handling
+ *
+ * Revision 1.6 2001/01/15 18:49:58 lord
+ * Improved exception handling
+ *
+ * Revision 1.5 2000/10/19 17:34:56 lord
+ * Import rationalisation
+ *
+ * Revision 1.4 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ * Revision 1.3 2000/08/03 16:38:24 lord
+ * Modifications to enable Cinema to run from jar file
+ *
+ * Revision 1.2 2000/07/18 10:37:08 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/05/30 16:05:54 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.java
new file mode 100644
index 0000000..edf41b8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaBootIdentifier.java
@@ -0,0 +1,76 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * CinemaBootIdentifier.java
+ *
+ *
+ * Created: Mon May 29 18:09:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaBootIdentifier.java,v 1.4 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaBootIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+ private CinemaBootIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaBootIdentifier CINEMA_BOOT =
+ new CinemaBootIdentifier( "uk.ac.man.bioinf.apps.cinema.CinemaBoot",
+ "Main Cinema Boot Class" );
+ public static final CinemaBootIdentifier CINEMA_SHARED =
+ new CinemaBootIdentifier( "uk.ac.man.bioinf.apps.cinema.CinemaShared",
+ "Shared Boot Class" );
+
+} // CinemaBootIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaBootIdentifier.java,v $
+ * Revision 1.4 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/09/15 17:26:51 lord
+ * Added shared factory boot
+ *
+ * Revision 1.2 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.1 2000/05/30 16:05:54 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.java
new file mode 100644
index 0000000..ec35a45
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaGuiModule.java
@@ -0,0 +1,167 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import javax.swing.JFrame;
+import javax.swing.JMenuBar;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentRuler;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaGuiModule.java
+ *
+ *
+ * Created: Fri May 26 21:04:15 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGuiModule.java,v 1.8 2001/04/11 17:04:41 lord Exp $
+ */
+
+public abstract class CinemaGuiModule extends CinemaModule
+{
+ public void destroy()
+ {
+ super.destroy();
+ gui = null;
+ }
+
+ // getters for the main cinema gui components. I may want to put
+ // setters for these here eventually, Im not sure.
+ public JFrame getFrame()
+ {
+ return getCore().getFrame();
+ }
+
+ private String mainTitleString;
+
+ public void setFrameTitle( String title )
+ {
+ if( mainTitleString == null ){
+ mainTitleString = getFrame().getTitle();
+ }
+
+ getFrame().setTitle( mainTitleString + ":- " + title );
+ }
+
+ public JAlignmentButtonPanel getRowHeaders()
+ {
+ return getCore().getRowHeaders();
+ }
+
+ public JMenuBar getJMenuBar()
+ {
+ return getCore().getJMenuBar();
+ }
+
+ public JScrollPane getScrollPane()
+ {
+ return getCore().getScrollPane();
+ }
+
+ public JPanel getRulerPanel()
+ {
+ return getCore().getRulerPanel();
+ }
+
+ public JAlignmentViewer getViewer()
+ {
+ return getCore().getViewer();
+ }
+
+ public JAlignmentRuler getRuler()
+ {
+ return getCore().getRuler();
+ }
+
+ public JTextField getStatusBar()
+ {
+ return getCore().getStatusBar();
+ }
+
+ public CinemaAlignmentFrame getAlignmentFrame()
+ {
+ return getCore().getAlignmentFrame();
+ }
+
+ private CinemaCoreGui gui;
+ private CinemaCoreGui getCore()
+ {
+ if( gui == null ){
+ gui = (CinemaCoreGui)getRequiredModule( CinemaModuleCoreIdentifier.CINEMA_CORE_GUI );
+ }
+ return gui;
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaModuleCoreIdentifier.CINEMA_CORE_GUI );
+ return list;
+ }
+
+} // CinemaGuiModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGuiModule.java,v $
+ * Revision 1.8 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2000/10/19 17:35:44 lord
+ * Added new method getAlignmentFrame
+ *
+ * Revision 1.6 2000/09/15 17:27:11 lord
+ * Now destroyable
+ *
+ * Revision 1.5 2000/09/11 14:00:31 lord
+ * Added support for setting frame title
+ *
+ * Revision 1.4 2000/06/27 13:37:38 lord
+ * Changed method names to resolve naming conflict
+ *
+ * Revision 1.3 2000/06/05 14:10:53 lord
+ * Removed version method again and made class abstract
+ *
+ * Revision 1.2 2000/06/05 14:09:49 lord
+ * Added version method
+ *
+ * Revision 1.1 2000/05/30 16:05:54 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaModule.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaModule.java
new file mode 100644
index 0000000..39bbba8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaModule.java
@@ -0,0 +1,224 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import java.awt.Color;
+import java.beans.PropertyChangeListener;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier;
+import uk.ac.man.bioinf.apps.xml.XMLModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel;
+
+
+/**
+ * CinemaModule.java
+ *
+ * Most modules for Cinema should extend this interface. It provides
+ * access to most of the functions of Cinema without being to tied to
+ * the main GUI components, which should insulate these modules from
+ * any changes which are made to it.
+ *
+ * I intend to include a few other methods here. I think that the
+ * CinemaModule should provide access to listeners for the cursor for
+ * instance, as this is a concept relatively divorced from that of the
+ * GUI.
+ *
+ * Created: Fri May 26 16:04:49 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaModule.java,v 1.7 2001/04/11 17:04:41 lord Exp $
+ */
+
+public abstract class CinemaModule extends XMLModule implements AlignmentEventProvider
+{
+
+ // These are the methods that define the state of the main window of
+ // cinema. At the moment that there are not many of them, though I
+ // expect that this will increase!
+ public SequenceAlignment getSequenceAlignment()
+ {
+ return getView().getSequenceAlignment();
+ }
+ /**
+ * Set the Sequence Alignment. Signals a property change event.
+ * @param seq
+ */
+ public void setSequenceAlignment( SequenceAlignment seq )
+ {
+ SequenceAlignment old = getSequenceAlignment();
+ getView().setSequenceAlignment( seq );
+ fireCinemaPropertyChange( CinemaProperties.SEQ_ALIGN.toString(), old, seq );
+ }
+
+ public ColorMap getColorMap()
+ {
+ return getView().getColorMap();
+ }
+
+ public void setColorMap( ColorMap map )
+ {
+ firePropertyChange( "colorMap", getColorMap(), map );
+ getView().setColorMap( map );
+ }
+
+ public AlignmentSelectionModel getAlignmentSelectionModel()
+ {
+ return getView().getAlignmentSelectionModel();
+ }
+
+ public void setAlignmentSelectionModel( AlignmentSelectionModel model )
+ {
+ firePropertyChange( "alignmentSelectionModel", getAlignmentSelectionModel(), model );
+ getView().setAlignmentSelectionModel( model );
+ }
+
+ /**
+ * This sets the colour that is used to display the sequence
+ * title. NOT the colour of the elements! This is usually done to
+ * display some linkage between sequences of the same colour.
+ * @param seq
+ * @param colour
+ */
+ public void setSequenceTitleColor( GappedSequence seq, Color colour )
+ {
+ getView().setSequenceTitleColor( seq, colour );
+ }
+
+ public void clearSequenceTitleColor( GappedSequence seq )
+ {
+ getView().clearSequenceTitleColor( seq );
+ }
+
+ public void sendStatusMessage( String message )
+ {
+ getView().sendStatusMessage( message );
+ }
+
+ public void fireCinemaPropertyChange( String name, Object old, Object newV )
+ {
+ getView().firePropertyChange( name, old, newV );
+ }
+
+ public void addCinemaPropertyChangeListener( PropertyChangeListener listener )
+ {
+ getView().addPropertyChangeListener( listener );
+ }
+
+ public void removeCinemaPropertyChangeListener( PropertyChangeListener listener )
+ {
+ getView().removePropertyChangeListener( listener );
+ }
+
+ public void addCinemaPropertyChangeListener( String propertyName, PropertyChangeListener listener )
+ {
+ getView().addPropertyChangeListener( propertyName, listener );
+ }
+
+ public void removeCinemaPropertyChangeListener( String propertyName, PropertyChangeListener listener )
+ {
+ getView().removePropertyChangeListener( propertyName, listener );
+ }
+
+ // implementation of AlignmentEventProvider interface
+ public void addAlignmentListener( AlignmentListener listener )
+ {
+ getView().addAlignmentListener( listener );
+ }
+
+ public void removeAlignmentListener( AlignmentListener listener )
+ {
+ getView().removeAlignmentListener( listener );
+ }
+
+ public void addVetoableAlignmentListener( VetoableAlignmentListener listener )
+ {
+ getView().addVetoableAlignmentListener( listener );
+ }
+
+ public void removeVetoableAlignmentListener( VetoableAlignmentListener listener )
+ {
+ getView().removeVetoableAlignmentListener( listener );
+ }
+
+ public void destroy()
+ {
+ super.destroy();
+ view = null;
+ }
+
+ private CinemaCoreView view;
+ private CinemaCoreView getView()
+ {
+ if( view == null ){
+ view = (CinemaCoreView)getRequiredModule( CinemaModuleCoreIdentifier.CINEMA_CORE_VIEW );
+ }
+ return view;
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaModuleCoreIdentifier.CINEMA_CORE_VIEW );
+ return list;
+ }
+} // CinemaModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaModule.java,v $
+ * Revision 1.7 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/01/15 18:50:16 lord
+ * Added access to alignment selection model
+ *
+ * Revision 1.5 2000/10/19 17:35:56 lord
+ * Improved event handling
+ *
+ * Revision 1.4 2000/09/15 17:27:04 lord
+ * Now destroyable
+ *
+ * Revision 1.3 2000/09/11 16:23:04 lord
+ * New status bar system. Wipes after 5 seconds of idle now.
+ *
+ * Revision 1.2 2000/06/05 14:11:13 lord
+ * Added CinemaPropertyChangeListener methods
+ *
+ * Revision 1.1 2000/05/30 16:05:54 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.java
new file mode 100644
index 0000000..6a6a8d9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaModuleFactoryInstance.java
@@ -0,0 +1,93 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaModuleCoreIdentifier;
+import uk.ac.man.bioinf.module.DefaultModuleFactoryInstance;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleIdentifier;
+
+
+/**
+ * CinemaModuleFactoryInstance.java
+ *
+ * This class adds some reporting functions to the superclass.
+ * Created: Wed Aug 2 13:47:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaModuleFactoryInstance.java,v 1.4 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaModuleFactoryInstance extends DefaultModuleFactoryInstance
+{
+ private CinemaCoreView coreView;
+
+ public Module load(ModuleIdentifier identifier) throws ModuleException
+ {
+ // we may not have started the core gui yet.
+ if( coreView != null && coreView.isStarted() ){
+ coreView.sendStatusMessage( "Loading module:- " + identifier.getModuleName() + " ... " );
+ }
+
+ Module retn = super.load( identifier );
+
+ // if this is the core gui that we have just started then store a
+ // copy of it for later use.
+ if( identifier == CinemaModuleCoreIdentifier.CINEMA_CORE_VIEW ){
+ coreView = (CinemaCoreView)retn;
+ }
+
+ if( coreView != null && coreView.isStarted() ){
+ coreView.sendStatusMessage( "Loading module:- " + identifier.getModuleName() + " ... Done" );
+ }
+
+ return retn;
+ }
+
+} // CinemaModuleFactoryInstance
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaModuleFactoryInstance.java,v $
+ * Revision 1.4 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/10/19 17:36:05 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/09/11 16:23:04 lord
+ * New status bar system. Wipes after 5 seconds of idle now.
+ *
+ * Revision 1.1 2000/08/02 14:53:37 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaProperties.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaProperties.java
new file mode 100644
index 0000000..d85ec39
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaProperties.java
@@ -0,0 +1,70 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import uk.ac.man.bioinf.util.AbstractEnumeration;
+
+
+/**
+ * CinemaProperties.java
+ *
+ * This are all of the property names that the CinemaModule signals
+ * changes for.
+ *
+ * Created: Fri Jun 2 17:51:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaProperties.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public final class CinemaProperties extends AbstractEnumeration
+{
+ private CinemaProperties( String toString )
+ {
+ super( toString );
+ }
+
+ public static final CinemaProperties SEQ_ALIGN = new CinemaProperties( "sequenceAlignment" );
+
+} // CinemaProperties
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaProperties.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/10/19 17:36:25 lord
+ * Made Strings final as they should have been originally
+ *
+ * Revision 1.1 2000/06/05 14:11:26 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaShared.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaShared.java
new file mode 100644
index 0000000..262a4b9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaShared.java
@@ -0,0 +1,48 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+
+
+/**
+ * CinemaShared.java
+ *
+ *
+ * Created: Tue Sep 12 17:22:26 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaShared.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaShared extends CinemaBoot
+{
+ public String fetchMainBootName()
+ {
+ return "cinema-shared.xml";
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java b/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java
new file mode 100644
index 0000000..3f25605
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/CinemaXMLParserFactory.java
@@ -0,0 +1,96 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema; // Package name inserted by JPack
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+import org.xml.sax.helpers.DefaultHandler;
+import org.xml.sax.helpers.XMLReaderFactory;
+import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
+import uk.ac.man.bioinf.apps.xml.XMLParserFactory;
+import uk.ac.man.bioinf.debug.Debug;
+
+
+/**
+ * CinemaXMLParserFactory.java
+ *
+ *
+ * Created: Mon Sep 18 18:59:17 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaXMLParserFactory.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaXMLParserFactory implements XMLParserFactory
+{
+
+ public XMLReader getXMLParser()
+ {
+ try{
+
+ XMLReader read = XMLReaderFactory.createXMLReader( "org.apache.xerces.parsers.SAXParser" );
+ read.setEntityResolver
+ ( new DefaultHandler(){
+ public InputSource resolveEntity( String publicId, String systemId ) throws SAXException
+ {
+ if( systemId.equals( "file:module.dtd" ) ){
+ return new InputSource( CinemaResources.getModuleDTDAsResource() );
+ }
+
+ return super.resolveEntity( publicId, systemId );
+ }
+ });
+ return read;
+ }
+ catch( Exception exp ){
+ if( Debug.debug )
+ Debug.throwable( this, exp );
+ }
+ return null;
+ }
+} // CinemaXMLParserFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaXMLParserFactory.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/18 12:09:23 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.1 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/changes.html b/src/uk/ac/man/bioinf/apps/cinema/changes.html
new file mode 100644
index 0000000..37cbfca
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/changes.html
@@ -0,0 +1,454 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+
+<html>
+ <head>
+ <title>Cinema Changes</title>
+ </head>
+
+ <body>
+ <h1>Cinema Changes</h1>
+
+ <a name = "contents"></a>
+ <h2>Contents</h2>
+ <ul
+ <li><a href = "#release-3_0_23">Release 3.0.23</a></li>
+ <li><a href = "#release-3_0_22">Release 3.0.22</a></li>
+ <li><a href = "#release-3_0_21">Release 3.0.21</a></li>
+ <li><a href = "#release-3_0_20">Release 3.0.20</a></li>
+ <li><a href = "#release-3_0_19">Release 3.0.19</a></li>
+ <li><a href = "#release-3_0_18">Release 3.0.18</a></li>
+ <li><a href = "#release-3_0_17">Release 3.0.17</a></li>
+ <li><a href = "#release-3_0_16">Release 3.0.16</a></li>
+ <li><a href = "#release-3_0_16">Release 3.0.16</a></li>
+ <li><a href = "#release-3_0_15">Release 3.0.15</a></li>
+ <li><a href = "#release-3_0_14">Release 3.0.14</a></li>
+ <li><a href = "#release-3_0_13">Release 3.0.13</a></li>
+ <li><a href = "#release-3_0_12">Release 3.0.12</a></li>
+ <li><a href = "#release-3_0_11">Release 3.0.11</a></li>
+ <li><a href = "#release-3_0_10">Release 3.0.10</a></li>
+ <li><a href = "#release-3_0_9">Release 3.0.9</a></li>
+ <li><a href = "#release-3_0_8">Release 3.0.8</a></li>
+ <li><a href = "#release-3_0_7">Release 3.0.7</a></li>
+ <li><a href = "#release-3_0_6">Release 3.0.6</a></li>
+ <li><a href = "#release-3_0_5">Release 3.0.5</a></li>
+ <li><a href = "#release-3_0_4">Release 3.0.4</a></li>
+ </ul>
+
+ <a name = "Release-"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ Input error handling has been improved
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_22"></a>
+ <h2>Release</h2>
+
+ <h3>Bug fixes</h3>
+
+ <p>Fixed classpath</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_21"></a>
+
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ Manifest support in build file.
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_20"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>The launch script now takes sequence files on the command
+ line.
+ <li>Some new documentation has been added.
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>Minor changes to the build process</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_19"></a>
+ <h2>Release 3.0.19</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Motif default extensions fixed on saving</li>
+ <li>Multiple consensus viewer fixed</li>
+ </ul>
+
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3.0.18"></a>
+ <h2>Release 3.0.18</h2>
+
+ This release should be the last one before we move toward Cinema
+ 3.1, and should be considered to be a "release
+ candidate".
+
+ <h3>User Visible Changes</h3>
+ A few small usability changes, and some additions!
+ <ul>
+ <li>Lots of colour schemes added. Also color-convert.el for
+ people who want to import more colour schemes.</li>
+ <li>Moved some of the menu items around.</li>
+ <li>Home directory is now selected by default for motif
+ save</li>
+ <li>Resize keep square is default</li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+ <ul>
+ <li>Stack trace dumping when gaps are removed from groups no
+ longer occurs</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_17"></a>
+ <h2>Release 3.0.17</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Now updates display correctly when consensus calculator is
+ changed.</li>
+ <li>Regular expression search now works correctly</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_16"></a>
+ <h2>Release 3.0.16</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>main.xml is no longer required</li>
+ <li>Error handling for options much improved</li>
+ </ul>
+
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_15"></a>
+ <h2>Release 3.0.15</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Renamed menu items</li>
+ </ul>
+
+ <h3>Code changes</h3>
+ <ul>
+ <li>Consensus and colour map factories now support a default
+ option.</li>
+ <li>Removed spam debug messages</li>
+ <li>Default file input parser now configurable</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_14"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Fixed bug in launch script which was totally preventing it
+ from working!</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_13"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>A large number of changes to the build process</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3.0.12"></a>
+ <h2>Release</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Updated version information correctly.
+ </li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3.0.11"></a>
+ <h2>Release-3.0.11</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>Changed build procedure, and directory structure associated
+ with it.</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3_0_10"></a>
+ <h2>Release-3.0.10</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Now as well as being to search for regexp's
+ there is a menu item which should enable you to actually
+ search for regexps</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ <a name = "Release-3.0.9"></a>
+ <h2>Release-3.0.9</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Cinema now remembers some details, such as window size,
+ element size and so on between different invocations</li>
+ <li>You can now search through sequences via regexp. The
+ interface is a little primitive at the moment, but will
+ improve. </li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+ <ul>
+ <li>Have now written ant scripts to build and install cinema</li>
+ <li>Installed persistance system</li>
+ <li>Altered module interface definition loading</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_8"></a>
+ <h2>Release-3.0.8</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>More status information is now printed out</li>
+ <li>Can now choose format on motif save</li>
+ <li>Can save only a single motif, as well as all of them</li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Fixed bug in PIR parser. Now writes 80 characters per line,
+ and no longer misses the last line</li>
+ <li>Enhancements to the XML loading process exception handling,
+ so problems are now a lot more informative</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <ul>
+ <li>Can now configure a single module from several different places</li>
+ <li>Can now load configuration from .cinema/config directory</li>
+ <li>Have completely re-organised the XML loading</li>
+ </ul>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "Release-3_0_7"></a>
+ <h2>Release-3.0.7</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Motifs are now automatically sorted in the MotifManager
+ dialog. This also impacts on the saved name.
+ </li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>A repaint bug has been fixed so that AlignmentSelections can
+ be seen to grow smaller.</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "release-3.0.6"></a>
+ <h2>Release-3.0.6</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>This time I have definiately removed all references to
+ treedraw!</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "release-3_0_5"></a>
+ <h2>Release-3.0.5</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <p>No user visible changes</p>
+
+ <h3>Bug fixes</h3>
+
+ <ul>
+ <li>Removed references to treedraw which is not currently
+ checked in</li>
+ </ul>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+
+ <a name = "release-3_0_4"></a>
+ <h2>Release 3.0.4</h2>
+
+ <h3>User Visible Changes</h3>
+
+ <ul>
+ <li>Support for multiple selection</li>
+ <li>Initial version of Motif Manager added</li>
+ </ul>
+
+ <h3>Bug fixes</h3>
+
+ <p>No bug fixes</p>
+
+ <h3>Code changes</h3>
+
+ <p>No code changes</p>
+
+ <a href ="#contents">Back to contents</a>
+ </body>
+</html>
+
+
+
+
+
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.java
new file mode 100644
index 0000000..ae05605
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/AminoAcidColorMapMetaData.java
@@ -0,0 +1,156 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * AminoAcidColorMapMetaData.java
+ *
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AminoAcidColorMapMetaData.java,v 1.4 2001/07/06 11:44:50 lord Exp $
+ */
+
+public class AminoAcidColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Amino Acid Color Scheme";
+
+ static
+ {
+ // color mapping
+ AminoAcid[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if (aa[i] == AminoAcid.GLYCINE)
+ colors[i] = new Color(255, 170, 136);
+ else if (aa[i] == AminoAcid.ALANINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.VALINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.LEUCINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.ISOLEUCINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.SERINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.CYSTEINE)
+ colors[i] = new Color(255, 255, 136);
+ else if (aa[i] == AminoAcid.THREONINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.METHIONINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.PHENYLALANINE)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.TYROSINE)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.TRYPTOPHAN)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.PROLINE)
+ colors[i] = new Color(255, 170, 136);
+ else if (aa[i] == AminoAcid.HISTIDINE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.LYSINE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.ARGININE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.ASPARTICACID)
+ colors[i] = new Color(255, 136, 136);
+ else if (aa[i] == AminoAcid.GLUTAMICACID)
+ colors[i] = new Color(255, 136, 136);
+ else if (aa[i] == AminoAcid.ASPARAGINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.GLUTAMINE)
+ colors[i] = new Color(136, 255, 136);
+ else
+ colors[i] = new Color(102, 102, 102);
+ }
+ colors[ aa.length ] = Color.white;
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+} // AminoAcidColorMapMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: AminoAcidColorMapMetaData.java,v $
+ * Revision 1.4 2001/07/06 11:44:50 lord
+ * Cosmetic
+ *
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:10:03 lord
+ * Updated due to change in MapMetaData interface.
+ *
+ * Revision 1.1 2000/07/26 13:29:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.java b/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.java
new file mode 100644
index 0000000..f4ea467
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorFactory.java
@@ -0,0 +1,170 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Properties;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaColorFactory.java
+ *
+ *
+ * Created: Fri Feb 9 11:49:21 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaColorFactory.java,v 1.5 2002/03/08 14:49:27 lord Exp $
+ */
+
+public class CinemaColorFactory extends CinemaModule
+{
+ private NullColorMapMetaData nullColorMD = new NullColorMapMetaData();
+ private HashMap metaDataHash = new HashMap();
+ private boolean debug = true;
+
+ public void start()
+ {
+ // We always want to provide a no color map option, and this
+ // provides it.
+ metaDataHash.put( nullColorMD.getColorMapName(), nullColorMD );
+
+ // we need to pull the MetaData instances from the information
+ // given in the config files. All of this stuff just instantiates
+ // Object for each MetaData class and puts it into a hash for
+ // latter.
+ Properties configProperties = getConfigProperties();
+
+ Iterator iter = configProperties.keySet().iterator();
+ while( iter.hasNext() ){
+ // declare this here so that we can access it in the catch block
+ String className;
+
+ try{
+ className = (String)iter.next();
+ Class metaDataClass = Class.forName( className );
+ ColorMapMetaData instance = (ColorMapMetaData)metaDataClass.newInstance();
+ metaDataHash.put( instance.getColorMapName(), instance );
+ instance.setModule( this );
+ }
+ catch( InstantiationException ie ){
+ if( Debug.debug || debug )
+ Debug.both( this, "Failed to instantiation class", ie );
+ }
+ catch( IllegalAccessException iae ){
+ if( Debug.debug || debug )
+ Debug.both( this, "Failed to access class", iae );
+ }
+ catch( ClassNotFoundException cnfe ){
+ if( Debug.debug || debug )
+ Debug.both( this, "Failed to find class", cnfe );
+ }
+ }
+ }
+
+ public void addMetaData( ColorMapMetaData colorMap )
+ {
+ }
+
+ /**
+ * Returns a meta data object for the given ColorMap.
+ * @param map
+ * @return
+ */
+ public ColorMapMetaData getMetaData( ColorMap map )
+ {
+ if( map == null ){
+ return getMetaData( (String)null );
+ }
+
+ return getMetaData( map.getName() );
+ }
+
+ public ColorMapMetaData getMetaData( String name )
+ {
+ if( name == null ){
+ name = "null";
+ }
+ return (ColorMapMetaData)metaDataHash.get( name );
+ }
+
+ public Iterator getColorMapIterator()
+ {
+ return metaDataHash.values().iterator();
+ }
+
+ public int getSize()
+ {
+ return metaDataHash.size();
+ }
+
+ public ColorMapMetaData getDefaultColorMapMetaData()
+ {
+ return nullColorMD;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaColorFactory.java,v 1.5 2002/03/08 14:49:27 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+ }
+} // CinemaColorFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaColorFactory.java,v $
+ * Revision 1.5 2002/03/08 14:49:27 lord
+ * Added local debug
+ *
+ * Revision 1.4 2001/05/08 17:37:38 lord
+ * Cosmetic changes
+ *
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/03/12 16:43:55 lord
+ * Updated module requirements
+ *
+ * Revision 1.1 2001/02/19 16:55:08 lord
+ * Have separated CinemaColorSelector into two. One factory for
+ * ColorMaps, one display module.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.java
new file mode 100644
index 0000000..eae9a84
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorIdentifier.java
@@ -0,0 +1,77 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * CinemaColorIdentifier.java
+ *
+ *
+ * Created: Sun May 28 22:34:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaColorIdentifier.java,v 1.4 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaColorIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaColorIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaColorIdentifier CINEMA_COLOR_FACTORY
+ = new CinemaColorIdentifier( "uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory",
+ "Provides the factory for color maps within cinema" );
+ public static final CinemaColorIdentifier CINEMA_COLOR_SELECTOR
+ = new CinemaColorIdentifier( "uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector",
+ "Provides the central selection system for colour map selection" );
+} // CinemaColorIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaColorIdentifier.java,v $
+ * Revision 1.4 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/02/19 16:55:08 lord
+ * Have separated CinemaColorSelector into two. One factory for
+ * ColorMaps, one display module.
+ *
+ * Revision 1.2 2000/07/26 13:30:35 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.1 2000/05/30 16:06:15 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.java b/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.java
new file mode 100644
index 0000000..428bee4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/CinemaColorSelector.java
@@ -0,0 +1,158 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Properties;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaColorSelector.java
+ *
+ * Created: Sun May 28 22:14:13 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaColorSelector.java,v 1.8 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaColorSelector extends CinemaGuiModule implements CinemaFramedActionProvider
+{
+ public void start()
+ {
+ setColorMap( getColorFactory().
+ getMetaData( AminoAcidColorMapMetaData.NAME ).
+ getInstance( getSequenceAlignment(), getViewer() ) );
+ }
+
+ public Action[] getActions( CinemaAlignmentFrame frame )
+ {
+
+ Action[] retn = new Action[ getColorFactory().getSize() ];
+
+ // the action for the null color map.
+ retn[ 0 ] = new ClosureAbstractAction( frame, "Colour Map off", "null" );
+
+ Iterator iter = getColorFactory().getColorMapIterator();
+ int i = 1;
+
+ while( iter.hasNext() ){
+ ColorMapMetaData md = (ColorMapMetaData)iter.next();
+ if( md != getColorFactory().getDefaultColorMapMetaData() ){
+ retn[ i++ ] = new ClosureAbstractAction( frame, md.getColorMapName(), md.getColorMapName() );
+ }
+ }
+
+ return retn;
+ }
+
+ class ClosureAbstractAction extends AbstractAction
+ {
+ private String colorMapName;
+ private ColorMapMetaData md;
+ private CinemaAlignmentFrame frame;
+
+ ClosureAbstractAction( CinemaAlignmentFrame frame, String title, String colorMapName )
+ {
+ super( title );
+ this.md = getColorFactory().getMetaData( colorMapName );
+ this.frame = frame;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ JAlignmentViewer viewer = frame.getViewer();
+
+ viewer.setColorMap( md.getInstance( getSequenceAlignment(), viewer ) );
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaColorSelector.java,v 1.8 2001/04/11 17:04:41 lord Exp $";
+ }
+
+ public CinemaColorFactory getColorFactory()
+ {
+ return ((CinemaColorFactory)getRequiredModule
+ ( CinemaColorIdentifier.CINEMA_COLOR_FACTORY ) );
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaColorIdentifier.CINEMA_COLOR_FACTORY );
+ return list;
+ }
+} // CinemaColorSelector
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaColorSelector.java,v $
+ * Revision 1.8 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2001/02/19 16:55:08 lord
+ * Have separated CinemaColorSelector into two. One factory for
+ * ColorMaps, one display module.
+ *
+ * Revision 1.6 2000/12/05 15:10:03 lord
+ * Updated due to change in MapMetaData interface.
+ *
+ * Revision 1.5 2000/10/19 17:37:44 lord
+ * Import rationalisation.
+ * Now extends CinemaFramedActionProvider. Not entirely happy with this,
+ * probably needs better coding!
+ *
+ * Revision 1.4 2000/07/26 13:31:15 lord
+ * Major rewrite, due to the addition of the ColorMapMetaData class. Now
+ * loads in ColorMaps from config files
+ *
+ * Revision 1.3 2000/06/13 11:14:00 lord
+ * Added new colour map
+ *
+ * Revision 1.2 2000/06/05 14:11:46 lord
+ * Added version method
+ *
+ * Revision 1.1 2000/05/30 16:06:15 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.java
new file mode 100644
index 0000000..7168e09
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/ColorMapMetaData.java
@@ -0,0 +1,93 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * ColorMapMetaData.java
+ *
+ * Many of the colour maps available need to be treated in different
+ * ways. So for instance some colour maps can use a single shared
+ * instance, others needs a new one for each alignment. It does not
+ * really make sense to try and encapsulate this sort of knowledge
+ * within the ColorMap class, but it is needed within Cinema...
+ *
+ * Created: Tue Jul 18 14:57:08 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ColorMapMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public interface ColorMapMetaData
+{
+
+ public void setModule( CinemaModule module );
+ /**
+ * This should return the string that ColorMap instances created via
+ * this class, return as their name, via the getName method
+ * @return the name
+ */
+ public String getColorMapName();
+
+ /**
+ * Returns a instance of this Color map for the given alignment
+ * instance.
+ * @return the ColorMap
+ */
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer );
+
+ /**
+ * Returns an instance of this type for this consensus sequence
+ * @param sequence the consensus sequence
+ * @return the ColorMap instance
+ */
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer );
+
+} // ColorMapMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: ColorMapMetaData.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:10:03 lord
+ * Updated due to change in MapMetaData interface.
+ *
+ * Revision 1.1 2000/07/26 13:29:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.java
new file mode 100644
index 0000000..f5285c4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/ColormapColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: ColormapColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class ColormapColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Colormap Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 255 , 170 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 255 , 170 , 136 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 136 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 136 , 136 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.java
new file mode 100644
index 0000000..44eb14e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/DefaultColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: DefaultColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class DefaultColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Default Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 255 , 170 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 255 , 170 , 136 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 136 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 136 , 136 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.java b/src/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.java
new file mode 100644
index 0000000..7daee87
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/GrayScaleVariance.java
@@ -0,0 +1,77 @@
+/*
+ * This software was written by Phillip Lord (p.lord at russet.org.uk)
+ * whilst at the University of Manchester.
+ *
+ * The initial code base is copyright the University of Manchester.
+ * Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorList;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.ColorStore;
+import uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+// Package name inserted by Jde-Package
+
+
+/**
+ * GrayScaleVariance.java
+ *
+ *
+ * Created: Fri Nov 30 13:58:29 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: GrayScaleVariance.java,v 1.1 2002/03/08 14:49:40 lord Exp $
+ */
+
+public class GrayScaleVariance implements ColorMapMetaData
+{
+
+
+ public void setModule( CinemaModule module )
+ {
+ // we don't need this module
+ }
+
+ public String getColorMapName()
+ {
+ return "GrayScale Variance (% ID)";
+ }
+
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return getCreateInstance( alignment );
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return getCreateInstance( sequence.getConsensusCalculator().getSequenceAlignment() );
+ }
+
+ private PercentIDVarianceColorMap getCreateInstance( SequenceAlignment alignment )
+ {
+ return new PercentIDVarianceColorMap
+ ( PercentageIDCalculatorManager.getDefaultInstance().getCalculator( alignment ),
+ ColorList.getGray50List() );
+ }
+} // GrayScaleVariance
+
+
+
+/*
+ * ChangeLog
+ * $Log: GrayScaleVariance.java,v $
+ * Revision 1.1 2002/03/08 14:49:40 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.java
new file mode 100644
index 0000000..d43c9bd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/InstancePerAlignmentColorMapMetaData.java
@@ -0,0 +1,92 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import java.util.WeakHashMap;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * InstancePerAlignmentColorMapMetaData.java
+ *
+ *
+ * Created: Wed Jul 19 14:50:50 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: InstancePerAlignmentColorMapMetaData.java,v 1.4 2001/04/11 17:04:41 lord Exp $
+ */
+
+public abstract class InstancePerAlignmentColorMapMetaData implements ColorMapMetaData
+{
+ private WeakHashMap instancesOfColorMap = new WeakHashMap();
+
+ protected abstract ColorMap createColorMapInstance( SequenceAlignment alignment );
+
+ public ColorMap getInstance( SequenceAlignment alignment )
+ {
+ Object retnObj = instancesOfColorMap.get( alignment );
+ if( retnObj == null ){
+ ColorMap retn = createColorMapInstance( alignment );
+ return retn;
+ }
+ return (ColorMap)retnObj;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence )
+ {
+ SequenceAlignment sa = sequence.getConsensusCalculator().getSequenceAlignment();
+ Object retnObj = instancesOfColorMap.get( sa );
+ if( retnObj == null ){
+ ColorMap retn = createColorMapInstance( sa );
+ instancesOfColorMap.put( sa, retn );
+ return retn;
+ }
+ return (ColorMap)retnObj;
+ }
+} // InstancePerAlignmentColorMapMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: InstancePerAlignmentColorMapMetaData.java,v $
+ * Revision 1.4 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/08 18:31:04 lord
+ * Changes to reflect alternation in ConsensusSequence interface
+ *
+ * Revision 1.2 2000/10/19 17:37:54 lord
+ * Import rationalisation.
+ *
+ * Revision 1.1 2000/07/26 13:29:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.java
new file mode 100644
index 0000000..3d93ae6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/IntenseColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: IntenseColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class IntenseColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Intense Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 153 , 102 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 153 , 102 , 0 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 255 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 0 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 0 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 0 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.java
new file mode 100644
index 0000000..1760a7b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/Js_TestColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: Js_TestColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class Js_TestColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Js_Test Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 255 , 240 , 240 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 0 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 106 , 106 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 76 , 76 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 171 , 255 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 195 , 80 , 76 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 195 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 225 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 225 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 106 , 255 , 76 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 195 , 110 , 76 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 46 , 195 , 46 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 76 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 46 , 255 , 46 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 255 , 225 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 255 , 84 , 255 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 0 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 59 , 255 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 0 , 0 , 0 );
+ else
+ colors[ i ] = new Color( 0 , 0 , 0 );
+ }
+ colors[ aa.length ] = new Color( 0 , 0 , 0 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.java
new file mode 100644
index 0000000..9916008
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/NullColorMapMetaData.java
@@ -0,0 +1,84 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * NullColorMapMetaData.java
+ *
+ *
+ * Created: Fri Jul 21 15:57:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NullColorMapMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class NullColorMapMetaData implements ColorMapMetaData
+{
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return "null";
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return null;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return null;
+ }
+} // NullColorMapMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: NullColorMapMetaData.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:10:03 lord
+ * Updated due to change in MapMetaData interface.
+ *
+ * Revision 1.1 2000/07/26 13:29:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.java
new file mode 100644
index 0000000..1b1a81c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/PedanticColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: PedanticColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class PedanticColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Pedantic Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 236 , 255 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 236 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 236 , 236 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 236 , 236 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 236 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 110 , 85 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 110 , 117 , 0 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 41 , 41 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 166 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 204 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 204 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 0 , 255 , 102 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 0 , 255 , 106 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 0 , 102 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 69 , 85 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 0 , 102 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.java
new file mode 100644
index 0000000..3c4be8a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/PercentageIDVarianceColorMapMetaData.java
@@ -0,0 +1,102 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * PercentageIDVarianceColorMapMetaData.java
+ *
+ *
+ * Created: Wed Jul 19 15:00:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: PercentageIDVarianceColorMapMetaData.java,v 1.6 2001/05/08 17:37:52 lord Exp $
+ */
+
+public class PercentageIDVarianceColorMapMetaData implements ColorMapMetaData
+{
+
+ public void setModule( CinemaModule module )
+ {
+ // we don't need this module
+ }
+
+ public String getColorMapName()
+ {
+ return "Variance (% ID)";
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return getCreateInstance( alignment );
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return getCreateInstance( sequence.getConsensusCalculator().getSequenceAlignment() );
+ }
+
+ private PercentIDVarianceColorMap getCreateInstance( SequenceAlignment alignment )
+ {
+ return new PercentIDVarianceColorMap
+ ( PercentageIDCalculatorManager.getDefaultInstance().getCalculator( alignment ) );
+ }
+} // PercentageIDVarianceColorMapMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: PercentageIDVarianceColorMapMetaData.java,v $
+ * Revision 1.6 2001/05/08 17:37:52 lord
+ * New external name.
+ *
+ * Revision 1.5 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/12/05 15:10:03 lord
+ * Updated due to change in MapMetaData interface.
+ *
+ * Revision 1.2 2000/11/08 18:31:14 lord
+ * Changes to reflect alternation in ConsensusSequence interface
+ *
+ * Revision 1.1 2000/07/26 13:29:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.java
new file mode 100644
index 0000000..78b15d6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/TaylorColorMapMetaData.java
@@ -0,0 +1,147 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: TaylorColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class TaylorColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Taylor Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 51 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 204 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 153 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 102 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 255 , 204 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 255 , 153 , 0 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 0 , 102 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 0 , 255 , 102 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 0 , 204 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 0 , 255 , 204 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 255 , 51 , 0 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 255 , 102 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 204 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 255 , 0 , 204 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 102 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 0 , 102 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 0 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+ public static void main( String[] args )
+ {
+ }
+
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.java
new file mode 100644
index 0000000..e113ff6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/ThreadedPercentageIDVarianceColorMapMetaData.java
@@ -0,0 +1,119 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents;
+import uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.PercentIDVarianceColorMap;
+import uk.ac.man.bioinf.gui.color.ThreadedColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * ThreadedPercentageIDVarianceColorMapMetaData.java
+ *
+ *
+ * Created: Fri Dec 1 16:54:24 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ThreadedPercentageIDVarianceColorMapMetaData.java,v 1.3 2001/05/08 17:37:59 lord Exp $
+ */
+
+public class ThreadedPercentageIDVarianceColorMapMetaData implements ColorMapMetaData
+{
+ private static final String NAME = "Variance (% ID Background)";
+
+ private CinemaModule module;
+
+ public void setModule( CinemaModule module )
+ {
+ this.module = module;
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return getCreateInstance( alignment, viewer );
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return getCreateInstance( sequence.getConsensusCalculator().getSequenceAlignment(), viewer );
+ }
+
+ private ThreadedColorMap getCreateInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ InvokerInternalQueue queue = new InvokerInternalQueue
+ ( (CinemaSystemEvents)module.getRequiredModule( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS ) );
+
+ // we want to fire the fast events as quickly as possible. This
+ // should allow coalescing of as many repaint requests as
+ // possible.
+ //queue.setOneAtATime( false );
+
+ // this code should win awards for the most wacky indentation.
+ return new ThreadedColorMap
+ ( viewer,
+ alignment,
+ new PercentIDVarianceColorMap
+ ( PercentageIDCalculatorManager.getDefaultInstance().getCalculator( alignment ) ),
+ queue )
+ {
+ public String getName()
+ {
+ return ThreadedPercentageIDVarianceColorMapMetaData.NAME;
+ }
+ };
+ }
+} // ThreadedPercentageIDVarianceColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: ThreadedPercentageIDVarianceColorMapMetaData.java,v $
+ * Revision 1.3 2001/05/08 17:37:59 lord
+ * New external name.
+ *
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/05 15:09:42 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.java
new file mode 100644
index 0000000..1a618e7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/VariableColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: VariableColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class VariableColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Variable Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 236 , 255 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 236 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 236 , 236 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 236 , 236 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 236 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 236 , 159 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 110 , 84 , 0 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 36 , 36 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 0 , 0 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 47 , 236 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 166 , 0 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 100 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 115 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 0 , 193 , 0 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 0 , 255 , 0 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 0 , 255 , 106 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 0 , 103 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 84 , 28 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 0 , 102 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.java
new file mode 100644
index 0000000..9a8967b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/VariationsColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: VariationsColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class VariationsColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Variations Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 255 , 145 , 95 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 255 , 145 , 95 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 87 , 68 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 87 , 68 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.java
new file mode 100644
index 0000000..3615252
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/WhiteColorMapMetaData.java
@@ -0,0 +1,86 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color; // Package name inserted by JPack
+
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.SingleColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * WhiteColorMapMetaData.java
+ *
+ *
+ * Created: Fri Feb 9 13:12:26 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: WhiteColorMapMetaData.java,v 1.2 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class WhiteColorMapMetaData implements ColorMapMetaData
+{
+ private SingleColorMap map = new SingleColorMap( Color.white, "white color map" );
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing needed.
+ }
+
+ public String getColorMapName()
+ {
+ return map.getName();
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence cons, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+} // WhiteColorMapMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: WhiteColorMapMetaData.java,v $
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 16:55:22 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.java
new file mode 100644
index 0000000..99b6568
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/color/ZenecaColorMapMetaData.java
@@ -0,0 +1,145 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: ZenecaColorMapMetaData.java,v 1.1 2001/07/06 11:45:21 lord Exp $
+ */
+
+public class ZenecaColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = "Zeneca Color Scheme";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+ else if ( aa[ i ] == AminoAcid.ALANINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASNORASP)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.CYSTEINE)
+ colors[ i ] = new Color( 255 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ASPARTICACID)
+ colors[ i ] = new Color( 255 , 136 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMICACID)
+ colors[ i ] = new Color( 255 , 136 , 136 );
+ else if ( aa[ i ] == AminoAcid.PHENYLALANINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.GLYCINE)
+ colors[ i ] = new Color( 255 , 170 , 136 );
+ else if ( aa[ i ] == AminoAcid.HISTIDINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ISOLEUCINE)
+ colors[ i ] = new Color( 255 , 255 , 68 );
+ else if ( aa[ i ] == AminoAcid.LYSINE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.LEUCINE)
+ colors[ i ] = new Color( 255 , 90 , 255 );
+ else if ( aa[ i ] == AminoAcid.METHIONINE)
+ colors[ i ] = new Color( 255 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.ASPARAGINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.PROLINE)
+ colors[ i ] = new Color( 255 , 170 , 136 );
+ else if ( aa[ i ] == AminoAcid.GLUTAMINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.ARGININE)
+ colors[ i ] = new Color( 136 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.SERINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.THREONINE)
+ colors[ i ] = new Color( 136 , 255 , 136 );
+ else if ( aa[ i ] == AminoAcid.VALINE)
+ colors[ i ] = new Color( 0 , 255 , 255 );
+ else if ( aa[ i ] == AminoAcid.TRYPTOPHAN)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.ANY)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else if ( aa[ i ] == AminoAcid.TYROSINE)
+ colors[ i ] = new Color( 255 , 136 , 255 );
+ else if ( aa[ i ] == AminoAcid.GLUORGLN)
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ else
+ colors[ i ] = new Color( 187 , 187 , 187 );
+ }
+ colors[ aa.length ] = new Color( 187 , 187 , 187 );
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.java b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.java
new file mode 100644
index 0000000..1f2add2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensus.java
@@ -0,0 +1,191 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.consensus; // Package name inserted by JPack
+import java.awt.Color;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Properties;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/*
+ * CinemaConsensus.java
+ *
+ *
+ * Created: Thu Jun 15 20:50:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaConsensus.java,v 1.13 2001/05/08 17:38:34 lord Exp $
+ */
+
+public class CinemaConsensus extends CinemaModule
+{
+ private HashMap metaDataHash = new HashMap();
+ private CinemaConsensusCalculatorMetaData defaultMetaData;
+
+ public void start()
+ {
+ // load the consensus calculators
+ Properties configProperties = getConfigProperties();
+
+ Iterator iter = configProperties.keySet().iterator();
+ while( iter.hasNext() ){
+ // declare this here so that we can access it in the catch block
+ String className;
+
+ try{
+ className = (String)iter.next();
+ Class metaDataClass = Class.forName( className );
+ CinemaConsensusCalculatorMetaData instance = (CinemaConsensusCalculatorMetaData)
+ metaDataClass.newInstance();
+ instance.setModule( this );
+
+ String value = configProperties.getProperty( className );
+ if( (value != null) && (value.equals( "VAL:default" )) ){
+ defaultMetaData = instance;
+ }
+
+ metaDataHash.put( instance.getConsensusCalculatorName(), instance );
+ }
+ catch( InstantiationException ie ){
+ if( Debug.debug )
+ Debug.both( this, "Failed to instantiation class", ie );
+ }
+ catch( IllegalAccessException iae ){
+ if( Debug.debug )
+ Debug.both( this, "Failed to access class", iae );
+ }
+ catch( ClassNotFoundException cnfe ){
+ if( Debug.debug )
+ Debug.both( this, "Failed to find class", cnfe );
+ }
+ }
+ }
+
+ public Collection getAllMetaData()
+ {
+ return metaDataHash.values();
+ }
+
+ public CinemaConsensusCalculatorMetaData getDefaultMetaData()
+ {
+ return defaultMetaData;
+ }
+
+ public CinemaConsensusCalculatorMetaData getMetaData( ConsensusSequence sequence )
+ {
+ return getMetaData( sequence.getConsensusCalculator() );
+ }
+
+ public CinemaConsensusCalculatorMetaData getMetaData( ConsensusCalculator calc )
+ {
+ return getMetaData( calc.getCalculatorName() );
+ }
+
+ public CinemaConsensusCalculatorMetaData getMetaData( String name )
+ {
+ System.out.println( "Getting meta data for name " + name );
+ return (CinemaConsensusCalculatorMetaData)metaDataHash.get( name );
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaConsensus.java,v 1.13 2001/05/08 17:38:34 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+ }
+} // CinemaConsensus
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaConsensus.java,v $
+ * Revision 1.13 2001/05/08 17:38:34 lord
+ * Now no longer requires consensus calculator and meta data to have
+ * the same name. Does this by storing the current meta data.
+ *
+ * Revision 1.12 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.11 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.10 2000/11/13 18:17:45 jns
+ * o removed an import statement left over from previous code - sorry
+ * this is really trivial and pretty pointless
+ *
+ * Revision 1.9 2000/11/09 16:19:26 lord
+ * Split into two. This now has nothing to do with the GUI display of the consensus's
+ *
+ * Revision 1.8 2000/11/08 18:31:34 lord
+ * Lots of changes, mostly to allow threaded calculation.
+ *
+ * Revision 1.7 2000/10/31 15:52:20 lord
+ * Put in a null check for ColorMaps
+ *
+ * Revision 1.6 2000/10/19 17:38:04 lord
+ * Import rationalisation.
+ *
+ * Revision 1.5 2000/10/11 16:54:04 lord
+ * Some debug code removed, and cosmetic changes.
+ *
+ * Revision 1.4 2000/09/27 16:21:42 jns
+ * o reverted back to single fast cell renderer, because of the ability
+ * to generate a multiplexer cell renderer that will render multiple cell
+ * renderers at one time.
+ *
+ * Revision 1.3 2000/09/18 17:50:26 jns
+ * o change of method name - setFastRenderers()
+ *
+ * Revision 1.2 2000/08/01 17:39:13 lord
+ * Worked out how to create an array in one line
+ *
+ * Revision 1.1 2000/08/01 17:20:23 lord
+ * Intial checkin
+ *
+ * Revision 1.2 2000/07/18 10:38:28 lord
+ * Now uses cursor less renderer as the cursor does not have any function here
+ *
+ * Revision 1.1 2000/06/27 13:38:19 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.java
new file mode 100644
index 0000000..9fbe0c4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusCalculatorMetaData.java
@@ -0,0 +1,67 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+/**
+ * CinemaConsensusCalculatorMetaData.java
+ *
+ *
+ * Created: Thu Jul 27 16:45:21 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaConsensusCalculatorMetaData.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public interface CinemaConsensusCalculatorMetaData
+{
+ public void setModule( CinemaModule module );
+
+ public String getConsensusCalculatorName();
+
+ public ConsensusSequence getInstance( SequenceAlignment alignment );
+}// CinemaConsensusCalculatorMetaData
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaConsensusCalculatorMetaData.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/08 18:31:56 lord
+ * Now has reference to module
+ *
+ * Revision 1.1 2000/08/01 17:20:23 lord
+ * Intial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.java b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.java
new file mode 100644
index 0000000..91df982
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusDisplay.java
@@ -0,0 +1,287 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.consensus; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.Iterator;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory;
+import uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier;
+import uk.ac.man.bioinf.apps.cinema.color.CinemaColorSelector;
+import uk.ac.man.bioinf.apps.cinema.color.ColorMapMetaData;
+import uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus;
+import uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusCalculatorMetaData;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents;
+import uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue;
+import uk.ac.man.bioinf.gui.viewer.CursorLessFastAlignmentViewerCellRenderer;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.SingleSequenceAlignment;
+
+
+/**
+ * CinemaConsensusDisplay.java
+ *
+ *
+ * Created: Thu Nov 9 15:06:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaConsensusDisplay.java,v 1.10 2001/05/22 15:50:18 lord Exp $
+ */
+
+public class CinemaConsensusDisplay extends CinemaGuiModule implements CinemaActionProvider, PropertyChangeListener
+{
+
+ private JAlignmentViewer consensusViewer;
+
+ public void load() throws ModuleException
+ {
+ consensusViewer = new JAlignmentViewer();
+ consensusViewer.setReadonly(true);
+ consensusViewer.setFastCellRenderer
+ (new CursorLessFastAlignmentViewerCellRenderer(consensusViewer));
+ }
+
+ public void start()
+ {
+ getRulerPanel().add( consensusViewer, BorderLayout.NORTH );
+
+ syncConsensusSequence( getConsensusModule().getDefaultMetaData(), getSequenceAlignment() );
+
+ syncConsensusColorMap();
+ getViewer().addPropertyChangeListener( this );
+ }
+
+ private static InvokerInternalQueue queue;
+
+ private ConsensusSequence cacheConsensus;
+ private CinemaConsensusCalculatorMetaData lastMetaData;
+ private void syncConsensusSequence( SequenceAlignment align )
+ {
+ syncConsensusSequence( lastMetaData, align );
+ }
+
+ private void syncConsensusSequence( CinemaConsensusCalculatorMetaData md,
+ SequenceAlignment align )
+ {
+ lastMetaData = md;
+ if( queue == null ){
+ queue = new InvokerInternalQueue
+ ( (CinemaSystemEvents)getRequiredModule( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS ) );
+ }
+
+ ConsensusSequence seq = md.getInstance( align );
+
+ consensusViewer.setSequenceAlignment
+ ( new SingleSequenceAlignment( seq ) );
+
+ if( cacheConsensus != null ){
+ cacheConsensus.destroy();
+ }
+
+ cacheConsensus = seq;
+
+ // jiggle the display a little bit.
+ // So I admit that this is a complete hack but it ensures that the
+ // consensus viewer is showing the correct bit. Other wise it
+ // shows the start of the sequence.
+ // Actually it also has the advantage of giving the user visual
+ // feedback, reassuring them that something has honestly changed.
+ Point point = getScrollPane().getViewport().getViewPosition();
+ point.setLocation( point.getX() + 1, point.getY() );
+ getScrollPane().getViewport().setViewPosition( point );
+ point.setLocation( point.getX() - 1, point.getY() );
+ getScrollPane().getViewport().setViewPosition( point );
+ }
+
+ private void syncConsensusColorMap()
+ {
+ if( getContext().isModuleAvailable( CinemaColorIdentifier.CINEMA_COLOR_FACTORY ) ){
+ try{
+ CinemaColorFactory select =
+ (CinemaColorFactory)getContext().getModule( CinemaColorIdentifier.CINEMA_COLOR_FACTORY );
+
+ ColorMapMetaData md = select.getMetaData( getViewer().getColorMap() );
+
+ // md might be null if the colour map did not itself come from
+ // the CinemaColorSelector module. This normally will only
+ // happen during development, but I might as well trap the
+ // error.
+ if( md != null ){
+ consensusViewer.setColorMap
+ ( md.getConsensusInstance
+ ( (ConsensusSequence)((SingleSequenceAlignment)consensusViewer.
+ getSequenceAlignment()).getSingleSequence(),
+ consensusViewer ) );
+
+ }
+ }
+ catch( ModuleException me ){
+ // its okay to just ignore this
+ }
+ }
+ }
+
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ if( event.getPropertyName().equals( "colorMap" ) ){
+ syncConsensusColorMap();
+ }
+
+ if( event.getPropertyName().equals( "cellWidth" ) ){
+ consensusViewer.setCellWidth( ((Integer)event.getNewValue()).intValue() );
+ }
+
+ if( event.getPropertyName().equals( "cellHeight" ) ){
+ consensusViewer.setCellHeight( ((Integer)event.getNewValue()).intValue() );
+ }
+
+ if( event.getPropertyName().equals( "sequenceAlignment" ) ){
+ syncConsensusSequence( getSequenceAlignment() );
+ }
+ }
+
+
+ public Action[] getActions()
+ {
+ Action[] retn = new Action[ getConsensusModule().getAllMetaData().size() + 1 ];
+
+ retn[ 0 ] = new ClosureAbstractAction
+ ( getConsensusModule().getDefaultMetaData(), "Default" );
+
+ Iterator iter = getConsensusModule().getAllMetaData().iterator();
+
+ int i = 1;
+ while( iter.hasNext() ){
+ CinemaConsensusCalculatorMetaData metad = (CinemaConsensusCalculatorMetaData)
+ iter.next();
+
+ retn[ i++ ] = new ClosureAbstractAction( metad );
+
+ }
+ return retn;
+ }
+
+
+ class ClosureAbstractAction extends AbstractAction
+ {
+ protected CinemaConsensusCalculatorMetaData md;
+ ClosureAbstractAction( CinemaConsensusCalculatorMetaData md, String title )
+ {
+ super( title );
+ this.md = md;
+ }
+
+ ClosureAbstractAction( CinemaConsensusCalculatorMetaData md )
+ {
+ super( md.getConsensusCalculatorName() );
+ this.md = md;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ CinemaConsensusDisplay.this.syncConsensusSequence
+ ( md, CinemaConsensusDisplay.this.getSequenceAlignment() );
+ CinemaConsensusDisplay.this.syncConsensusColorMap();
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaConsensusDisplay.java,v 1.10 2001/05/22 15:50:18 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaConsensusIdentifier.CINEMA_CONSENSUS );
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+ }
+
+ private CinemaConsensus cons;
+ public CinemaConsensus getConsensusModule()
+ {
+ if( cons == null ){
+ cons = (CinemaConsensus)getRequiredModule( CinemaConsensusIdentifier.CINEMA_CONSENSUS );
+ }
+ return cons;
+ }
+} // CinemaConsensusDisplay
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaConsensusDisplay.java,v $
+ * Revision 1.10 2001/05/22 15:50:18 lord
+ * Now jiggles the display a bit when the consensus sequence calculator
+ * is changed. Its a bit of a hack but it works.
+ *
+ * Revision 1.9 2001/05/08 17:38:59 lord
+ * Accesses default meta data by new method
+ *
+ * Revision 1.8 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2001/02/19 16:55:45 lord
+ * Modified due to changes in Color modules.
+ *
+ * Revision 1.6 2000/12/20 17:43:28 jns
+ * o set the ConsensusDisplay to be readonly
+ *
+ * Revision 1.5 2000/12/12 13:02:47 jns
+ * o changing renderer to employ the multiplexer - thus it keeps in step
+ * with the main alignment
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/12/05 15:10:57 lord
+ * Mostly updated due to changes in ColorMap syncing.
+ *
+ * Revision 1.2 2000/11/13 18:18:28 jns
+ * o removed the border because it looked a bit ugly, after I had altered
+ * the BAVUI to take account of insets
+ *
+ * Revision 1.1 2000/11/09 16:17:37 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.java
new file mode 100644
index 0000000..9e700a4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/consensus/CinemaConsensusIdentifier.java
@@ -0,0 +1,75 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * CinemaConsensusIdentifier.java
+ *
+ *
+ * Created: Mon Jul 24 18:55:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaConsensusIdentifier.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaConsensusIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaConsensusIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaConsensusIdentifier CINEMA_CONSENSUS
+ = new CinemaConsensusIdentifier( "uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus",
+ "Provides a consensus sequence" );
+
+
+ public static final CinemaConsensusIdentifier CINEMA_CONSENSUS_DISPLAY
+ = new CinemaConsensusIdentifier( "uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusDisplay",
+ "Provides a consensus sequence" );
+} // CinemaConsensusIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaConsensusIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/09 16:20:26 lord
+ * New identifier
+ *
+ * Revision 1.1 2000/08/01 17:20:23 lord
+ * Intial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.java
new file mode 100644
index 0000000..22e6f9f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/consensus/PercentageIDConsensusCalculatorMetaData.java
@@ -0,0 +1,105 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusCalculator;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.consensus.DefaultConsensusSequence;
+import uk.ac.man.bioinf.analysis.consensus.PercentageIDConsensus;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * PercentageIDConsensusCalculatorMetaData.java
+ *
+ *
+ * Created: Thu Jul 27 16:46:59 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: PercentageIDConsensusCalculatorMetaData.java,v 1.6 2001/05/08 17:39:16 lord Exp $
+ */
+
+public class PercentageIDConsensusCalculatorMetaData implements CinemaConsensusCalculatorMetaData
+{
+ private static PercentageIDConsensusCalculatorMetaData inst =
+ new PercentageIDConsensusCalculatorMetaData();
+
+ public static PercentageIDConsensusCalculatorMetaData getMetaDataInstance()
+ {
+ return inst;
+ }
+
+ protected ConsensusCalculator getCalculatorInstance( SequenceAlignment alignment )
+ {
+ return new PercentageIDConsensus
+ ( PercentageIDCalculatorManager.getDefaultInstance().getCalculator( alignment ) );
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // no implementation needed.
+ }
+
+ public ConsensusSequence getInstance( SequenceAlignment alignment )
+ {
+ return new DefaultConsensusSequence( getCalculatorInstance( alignment ) );
+ }
+
+ public String getConsensusCalculatorName()
+ {
+ return "Consensus (% ID)";
+ }
+} // PercentageIDConsensusCalculatorMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: PercentageIDConsensusCalculatorMetaData.java,v $
+ * Revision 1.6 2001/05/08 17:39:16 lord
+ * New external names.
+ *
+ * Revision 1.5 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/11/08 18:32:36 lord
+ * Removed calculatable nonsense which was not working anyway and
+ * replaced it with a much simpler, and more effective method
+ *
+ * Revision 1.2 2000/10/11 16:54:19 lord
+ * Added documentation
+ *
+ * Revision 1.1 2000/08/01 17:20:23 lord
+ * Intial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.java b/src/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.java
new file mode 100644
index 0000000..38222cd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/consensus/ThreadedPercentageIDConsensusCalculatorMetaData.java
@@ -0,0 +1,98 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.consensus; // Package name inserted by JPack
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.consensus.ThreadedConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents;
+import uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * ThreadedPercentageIDConsensusCalculatorMetaData.java
+ *
+ *
+ * Created: Wed Nov 8 15:01:52 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ThreadedPercentageIDConsensusCalculatorMetaData.java,v 1.6 2001/05/08 17:39:16 lord Exp $
+ */
+
+public class ThreadedPercentageIDConsensusCalculatorMetaData
+ extends PercentageIDConsensusCalculatorMetaData
+{
+ private static final String NAME = "Consensus (% ID Background)";
+
+ private CinemaModule module;
+
+ public void setModule( CinemaModule module )
+ {
+ this.module = module;
+ }
+
+ public ConsensusSequence getInstance( SequenceAlignment alignment )
+ {
+ InvokerInternalQueue queue = new InvokerInternalQueue
+ ( (CinemaSystemEvents)module.getRequiredModule( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS ) );
+
+ return new ThreadedConsensusSequence( getCalculatorInstance( alignment ), queue );
+ }
+
+ public String getConsensusCalculatorName()
+ {
+ return NAME;
+ }
+} // ThreadedPercentageIDConsensusCalculatorMetaData
+
+
+
+/*
+ * ChangeLog
+ * $Log: ThreadedPercentageIDConsensusCalculatorMetaData.java,v $
+ * Revision 1.6 2001/05/08 17:39:16 lord
+ * New external names.
+ *
+ * Revision 1.5 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/12/05 15:18:06 lord
+ * Now has one InvokerInternalQueue per instance
+ *
+ * Revision 1.2 2000/11/09 16:20:41 lord
+ * Removed debug output
+ *
+ * Revision 1.1 2000/11/08 18:33:02 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.java b/src/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.java
new file mode 100644
index 0000000..1271c02
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListCellRenderer.java
@@ -0,0 +1,82 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import javax.swing.DefaultListCellRenderer;
+import java.awt.Component;
+import javax.swing.JList;
+import uk.ac.man.bioinf.sequence.Sequence;
+
+
+/**
+ * AlignmentToListCellRenderer.java
+ *
+ *
+ * Created: Tue May 16 18:02:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentToListCellRenderer.java,v 1.3 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class AlignmentToListCellRenderer extends DefaultListCellRenderer
+{
+ public Component getListCellRendererComponent(
+ JList list,
+ Object value,
+ int index,
+ boolean isSelected,
+ boolean cellHasFocus)
+ {
+ if( value == null ){
+ return super.getListCellRendererComponent
+ ( list, "", index, isSelected, cellHasFocus );
+ }
+
+ Sequence seq = (Sequence)value;
+ String resString = seq.getIdentifier().getTitle();
+ if( resString == null ) resString = "Null";
+ return super.getListCellRendererComponent
+ ( list, resString, index, isSelected, cellHasFocus );
+ }
+} // AlignmentToListCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentToListCellRenderer.java,v $
+ * Revision 1.3 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/07/18 10:37:57 lord
+ * Updated due to move from biointerface
+ *
+ * Revision 1.1 2000/05/18 17:13:10 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.java b/src/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.java
new file mode 100644
index 0000000..2f2e5cf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/AlignmentToListModel.java
@@ -0,0 +1,92 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import javax.swing.event.ListDataListener;
+import javax.swing.AbstractListModel;
+
+
+/**
+ * AlignmentToListModel.java
+ *
+ *
+ * Created: Tue May 16 17:55:45 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentToListModel.java,v 1.2 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class AlignmentToListModel extends AbstractListModel
+{
+ private SequenceAlignment alignment;
+
+ public AlignmentToListModel( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ }
+
+ public int getSize()
+ {
+ return alignment.getNumberSequences();
+ }
+
+ public Object getElementAt( int index )
+ {
+ try{
+ return alignment.getSequenceAt( index + 1 );
+ }
+ catch( ArrayIndexOutOfBoundsException ai ){
+ System.out.println( "No sequence at " + index );
+ return null;
+ }
+ }
+
+ public void addListDataListener( ListDataListener l )
+ {
+ //throw new Error( "Time Travel Error: Attempt to use code I have not written yet" );
+ }
+
+ public void removeListDataListener( ListDataListener l )
+ {
+ //throw new Error( "Time Travel Error: Attempt to use code I have not written yet" );
+ }
+} // AlignmentToListModel
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentToListModel.java,v $
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/18 17:13:10 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.java
new file mode 100644
index 0000000..7931023
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaActionProvider.java
@@ -0,0 +1,58 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import javax.swing.Action;
+
+/**
+ * CinemaActionProvider.java
+ *
+ *
+ * Created: Tue May 16 16:32:25 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaActionProvider.java,v 1.2 2001/04/11 17:04:41 lord Exp $
+ */
+
+public interface CinemaActionProvider
+{
+ public Action[] getActions();
+}// CinemaActionProvider
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaActionProvider.java,v $
+ * Revision 1.2 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/18 17:13:10 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.java
new file mode 100644
index 0000000..414cab9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreGui.java
@@ -0,0 +1,297 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.WindowEvent;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JFrame;
+import javax.swing.JMenuBar;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import uk.ac.man.bioinf.apps.cinema.Cinema;
+import uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier;
+import uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame;
+import uk.ac.man.bioinf.apps.systemevents.SystemEvent;
+import uk.ac.man.bioinf.apps.systemevents.SystemListener;
+import uk.ac.man.bioinf.apps.systemevents.SystemVetoException;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentRuler;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaCoreGui.java
+ *
+ * This module defines the core Gui for cinema. It gives access to all
+ * of the main components that it defines, and get/set methods for
+ * these. This is meant to be a pretty low level module. Generally
+ * other modules should not use this unless absolutely
+ * necessary. Rather the CinemaCoreView module should be used instead.
+ *
+ * At the moment set access has not been provided to any of the
+ * components. I may change this if is needed.
+ *
+ * Created: Wed Apr 19 16:58:08 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaCoreGui.java,v 1.17 2001/05/08 17:39:31 lord Exp $
+ */
+
+public class CinemaCoreGui extends Module implements SystemListener, CinemaActionProvider
+{
+ private CinemaAlignmentFrame alignmentFrame;
+ private JTextField statusBar;
+
+ public void load() throws ModuleException
+ {
+ String title = "Cinema " + VersionInformation.getVersionNumber()
+ + " by " + VersionInformation.getAuthorString();
+
+ alignmentFrame = new CinemaAlignmentFrame( "cinema.core.main.frame", title, true ){
+ public void processWindowEvent( WindowEvent event )
+ {
+ if( event.getID() == WindowEvent.WINDOW_CLOSING ){
+ // (PENDING:- PL) This needs to call the external "System
+ // Event Module".
+ attemptSystemExit();
+ }
+ else{
+ super.processWindowEvent( event );
+ }
+ }
+ };
+
+
+ statusBar = new JTextField();
+ statusBar.setEditable( false );
+ statusBar.setBackground( alignmentFrame.getBackground() );
+ statusBar.setForeground( Color.black );
+
+ alignmentFrame.getMainPanel().add( statusBar, BorderLayout.SOUTH );
+ }
+
+ public void start()
+ {
+ getSystemEventModule().addSystemEventListener( this );
+ alignmentFrame.setDefaultSize( 400, 400 );
+ }
+
+ public void destroy()
+ {
+ super.destroy();
+ // kill everything in sight which might prevent GC...
+ alignmentFrame.setVisible( false );
+ alignmentFrame.dispose();
+ statusBar = null;
+ alignmentFrame = null;
+ }
+
+ public void systemEventOccured( SystemEvent event ) throws SystemVetoException
+ {
+ int response = JOptionPane.showConfirmDialog
+ ( alignmentFrame, "Are you sure you want to close this application",
+ "Kill application", JOptionPane.YES_NO_OPTION );
+ if ( response == JOptionPane.NO_OPTION ){
+ throw new SystemVetoException
+ ( "User does not want to shutdown", event );
+ }
+ else{
+ return;
+ }
+ }
+
+ public int systemListenerPriority()
+ {
+ return VETO_DUE_TO_USER_REQUEST;
+ }
+
+ //getters and setters
+ public JFrame getFrame()
+ {
+ return alignmentFrame;
+ }
+
+ public JAlignmentButtonPanel getRowHeaders()
+ {
+ return alignmentFrame.getRowHeaders();
+ }
+
+ public JMenuBar getJMenuBar()
+ {
+ return alignmentFrame.getJMenuBar();
+ }
+
+ public JScrollPane getScrollPane()
+ {
+ return alignmentFrame.getScrollPane();
+ }
+
+ public JPanel getRulerPanel()
+ {
+ return alignmentFrame.getRulerPanel();
+ }
+
+ public JAlignmentViewer getViewer()
+ {
+ return alignmentFrame.getViewer();
+ }
+
+ public JAlignmentRuler getRuler()
+ {
+ return alignmentFrame.getRuler();
+ }
+
+ public JTextField getStatusBar()
+ {
+ return statusBar;
+ }
+
+ public CinemaAlignmentFrame getAlignmentFrame()
+ {
+ return alignmentFrame;
+ }
+
+ public void attemptSystemExit()
+ {
+ getSystemEventModule().fireSystemExit( 0 );
+ }
+
+ public Action[] getActions()
+ {
+ try{
+ // this module provides a cute quit/exit thing, which allows
+ // shutting down multiple isntances of cinema.
+ CinemaSharedQuitExit sQE = (CinemaSharedQuitExit)Cinema.
+ getSharedModuleInstance( CinemaSharedIdentifier.CINEMA_QUIT_EXIT );
+ return sQE.getActions( this );
+ }
+ catch( ModuleException mde ){
+ // oh dear.
+ }
+
+ // never mind, the nifty shut down is non essential and this is a
+ // simpler and works just as well.
+ Action[] retn = new Action[ 1 ];
+ retn[ 0 ] = new AbstractAction(){
+ public void actionPerformed( ActionEvent event )
+ {
+ attemptSystemExit();
+ }
+ };
+ return retn;
+ }
+
+ private CinemaSystemEvents getSystemEventModule()
+ {
+ return (CinemaSystemEvents)getRequiredModule( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaCoreGui.java,v 1.17 2001/05/08 17:39:31 lord Exp $";
+ }
+
+} // CinemaCoreGui
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaCoreGui.java,v $
+ * Revision 1.17 2001/05/08 17:39:31 lord
+ * Removed spam debug statements.
+ *
+ * Revision 1.16 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.15 2001/02/19 16:56:16 lord
+ * Added optionability
+ *
+ * Revision 1.14 2001/01/31 17:41:20 lord
+ * Made a little more robust. Essentially if the nifty shared shut down
+ * thing fails, I just have a single Exit button.
+ *
+ * Revision 1.13 2000/12/13 16:27:56 lord
+ * Removed debug statement
+ *
+ * Revision 1.12 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.11 2000/10/19 17:38:23 lord
+ * Access to CinemaAlignmentFrame provided
+ *
+ * Revision 1.10 2000/09/15 17:28:54 lord
+ * Now destroyable.
+ * Delegates Close, and Exit functionality to a module shared amoung
+ * all instances
+ *
+ * Revision 1.9 2000/08/02 14:54:20 lord
+ * Removed test status bar message
+ *
+ * Revision 1.8 2000/07/18 10:38:53 lord
+ * Import rationalisation
+ *
+ * Revision 1.7 2000/06/27 13:39:15 lord
+ * Now uses CinemaAlignmentFrame, so much of the code has been moved to
+ * that class
+ *
+ * Revision 1.6 2000/05/30 16:09:01 lord
+ * Rationalised imports.
+ * Added status bar.
+ * Changes due to completion of the module package
+ * Now also ActionProvider
+ *
+ * Revision 1.5 2000/05/24 15:35:17 lord
+ * Sorted imports
+ * Added row headers code
+ *
+ * Revision 1.4 2000/05/18 17:12:52 lord
+ * Support for row headers
+ *
+ * Revision 1.3 2000/05/15 16:21:02 lord
+ * fixed close down bug
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.java
new file mode 100644
index 0000000..997be67
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreIdentifier.java
@@ -0,0 +1,92 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+
+/**
+ * CinemaCoreIdentifier.java
+ *
+ *
+ * Created: Sun May 7 18:16:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaCoreIdentifier.java,v 1.6 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaCoreIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+ private CinemaCoreIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaCoreIdentifier CINEMA_GO
+ = new CinemaCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaGo",
+ "Following the Loading this module makes Cinema Visible" );
+ public static final CinemaCoreIdentifier CINEMA_SYSTEM_EVENTS
+ = new CinemaCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents",
+ "Provides system event support for Cinema" );
+ public static final CinemaCoreIdentifier CINEMA_MENU_SYSTEM
+ = new CinemaCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaMenuSystem",
+ "Provides a configurable menu system for cinema" );
+ public static final CinemaCoreIdentifier CINEMA_SEQUENCE_MENU
+ = new CinemaCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu",
+ "Provides a menu system for the sequence buttons" );
+ // public static final CinemaCoreIdentifier CINEMA_CONSENSUS
+ // = new CinemaCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaConsensus",
+ //"Provides the consensus tracker for cinema" );
+} // CinemaCoreIdentifiers
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaCoreIdentifier.java,v $
+ * Revision 1.6 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.4 2000/06/27 13:39:36 lord
+ * Added Cinema Consensus identifier
+ *
+ * Revision 1.3 2000/05/30 16:10:10 lord
+ * Removed core view and core gui to CinemaModuleCoreIdentifier
+ * Added some more modules
+ *
+ * Revision 1.2 2000/05/24 15:35:54 lord
+ * Added new method in ModuleIdentifier interface
+ *
+ * Revision 1.1 2000/05/15 16:21:13 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.java
new file mode 100644
index 0000000..25184d8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaCoreView.java
@@ -0,0 +1,301 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import java.awt.Color;
+import java.util.Dictionary;
+import javax.swing.JLabel;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel;
+
+
+/**
+ * CinemaCoreView.java
+ *
+ * This class provides an easy interface to many of the display
+ * functions of Cinema. (PENDING:- PL) In time this should actually be
+ * turned into an interface. The idea is that all modules should use
+ * this class rather than the CinemaCoreGui class, because there is
+ * nothing here which refers to swing which means that we could
+ * replace the gui implementation with an entirely different gui, and
+ * still reuse many of the modules.
+ *
+ * Created: Wed Apr 19 22:00:36 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaCoreView.java,v 1.13 2001/04/11 17:04:41 lord Exp $
+ */
+
+public class CinemaCoreView extends CinemaGuiModule implements AlignmentEventProvider, AlignmentListener
+{
+ private AlignmentListenerSupport alignSupp = new AlignmentListenerSupport();
+
+ public void start()
+ {
+ getViewer().getSequenceAlignment().addAlignmentListener( this );
+ }
+
+ public void destroy()
+ {
+ super.destroy();
+ // call an interrupt. The thread should then shut itself down
+ if( statusWiperThread != null ){
+ statusWiperThread.interrupt();
+ }
+ }
+
+ public void setSequenceAlignment( SequenceAlignment alignment )
+ {
+ SequenceAlignment oldAlign = getViewer().getSequenceAlignment();
+
+ getViewer().setSequenceAlignment( alignment );
+ getRuler().setSequenceAlignment( alignment );
+ getRowHeaders().setSequenceAlignment( alignment );
+ offsetFirstLabel();
+ }
+
+ public SequenceAlignment getSequenceAlignment()
+ {
+ return getViewer().getSequenceAlignment();
+ }
+
+ public void setAlignmentSelectionModel( AlignmentSelectionModel model )
+ {
+ getViewer().setSelectionModel( model );
+ }
+
+ public AlignmentSelectionModel getAlignmentSelectionModel()
+ {
+ return getViewer().getSelectionModel();
+ }
+
+ public void setColorMap( ColorMap map )
+ {
+ getViewer().setColorMap( map );
+ }
+
+ public ColorMap getColorMap()
+ {
+ return getViewer().getColorMap();
+ }
+
+ public void setSequenceTitleColor( GappedSequence seq, Color colour )
+ {
+ getRowHeaders().setSequenceColor( seq, colour );
+ }
+
+ public void clearSequenceTitleColor( GappedSequence seq )
+ {
+ getRowHeaders().clearSequenceColor( seq );
+ }
+
+
+ // this stuff implements a simple status bar clearer. The status
+ // messages stay up for a maximium of five seconds. Its implemented
+ // by polling the time stamp every .5 seconds, although perhaps it
+ // should be replaced with a "wait/notify" mechanism.
+ /**
+ * Send a message to the status bar. This message should be for
+ * minor information only as it can get overrun at any stage.
+ *
+ * @param message
+ */
+ public void sendStatusMessage( String message )
+ {
+ // start the wiper thread if it hasnt been already.
+ if( statusWiperThread == null ){
+ statusWiperThread = new Thread(){
+ public void run()
+ {
+ while( !CinemaCoreView.this.isDestroyed() ){
+ try{
+ Thread.sleep( 500 );
+ if( (System.currentTimeMillis() -
+ CinemaCoreView.this.getStatusUpdateTimestamp())
+ > 5000 ){
+ CinemaCoreView.this.setStatusUpdateTimestamp( System.currentTimeMillis() );
+ CinemaCoreView.this.clearStatusMessage();
+
+ }
+ }
+ catch( InterruptedException ie ){
+ // safe to ignore this.
+ }
+ }
+ }
+ };
+ statusWiperThread.start();
+ }
+ // update the time stamp and set the message
+ setStatusUpdateTimestamp( System.currentTimeMillis() );
+ setStatusMessage( message );
+ }
+
+ private long getStatusUpdateTimestamp()
+ {
+ // need to sync this as the time stamp is a long and access is
+ // not guarenteed to be atomic.
+ synchronized( statusWiperThread ){
+ return lastStatusUpdateTimestamp;
+ }
+ }
+
+ private void setStatusUpdateTimestamp( long newTimeStamp )
+ {
+ synchronized( statusWiperThread ){
+ lastStatusUpdateTimestamp = newTimeStamp;
+ }
+ }
+
+ // this is the thread that wipes the status bar clean.
+ private Thread statusWiperThread;
+ // the time stamp for the access.
+ private long lastStatusUpdateTimestamp;
+
+ private void clearStatusMessage()
+ {
+ if( !getStatusBar().getText().equals( "" ) ){
+ setStatusMessage( "" );
+ }
+ }
+
+ private void setStatusMessage( String message )
+ {
+ if( Debug.debug ){
+ Debug.message( this, "Status Message: " + message );
+ }
+ getStatusBar().setText( message );
+ getStatusBar().repaint();
+ getStatusBar().validate();
+ }
+
+ private void offsetFirstLabel()
+ {
+ // off set the 1 label so it fits on screen
+ Dictionary dic = getRuler().getLabelTable();
+ JLabel oneLabel = (JLabel)dic.get( new Integer( 1 ) );
+ oneLabel.setText( " 1" );
+ getRuler().setLabelTable( dic );
+ }
+
+ // implementation of AlignmentListener
+ public void changeOccurred( AlignmentEvent event )
+ {
+ alignSupp.fireAlignmentEvent( event );
+ }
+
+ // implementation of AlignmentEventProvider interface
+ public void addAlignmentListener( AlignmentListener listener )
+ {
+ alignSupp.addAlignmentListener( listener );
+ }
+
+ public void removeAlignmentListener( AlignmentListener listener )
+ {
+ alignSupp.removeAlignmentListener( listener );
+ }
+
+ public void addVetoableAlignmentListener( VetoableAlignmentListener listener )
+ {
+ alignSupp.addVetoableAlignmentListener( listener );
+ }
+
+ public void removeVetoableAlignmentListener( VetoableAlignmentListener listener )
+ {
+ alignSupp.removeVetoableAlignmentListener( listener );
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaModuleCoreIdentifier.CINEMA_CORE_GUI );
+ return list;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaCoreView.java,v 1.13 2001/04/11 17:04:41 lord Exp $";
+ }
+} // CinemaCoreView
+
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaCoreView.java,v $
+ * Revision 1.13 2001/04/11 17:04:41 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.12 2001/01/27 16:53:14 lord
+ * cosmetic
+ *
+ * Revision 1.11 2001/01/15 18:50:30 lord
+ * Added access to alignment selection model
+ *
+ * Revision 1.10 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.9 2000/10/19 17:38:47 lord
+ * Moved all event handling upto CinemaModule
+ *
+ * Revision 1.8 2000/09/15 17:29:16 lord
+ * Now destroyable
+ *
+ * Revision 1.7 2000/09/11 16:23:04 lord
+ * New status bar system. Wipes after 5 seconds of idle now.
+ *
+ * Revision 1.6 2000/06/05 14:12:16 lord
+ * Property change support on setAlignment method
+ *
+ * Revision 1.5 2000/05/30 16:11:06 lord
+ * Changes due to introduction of CinemaModule.
+ * Added Status bar support
+ *
+ * Revision 1.4 2000/05/24 15:36:22 lord
+ * Sorted imports.
+ * Added accessor function
+ *
+ * Revision 1.3 2000/05/18 17:12:34 lord
+ * Support for row headers
+ *
+ * Revision 1.2 2000/05/15 16:21:45 lord
+ * Added a load of getter setter methods
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.java
new file mode 100644
index 0000000..7ced448
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaFramedActionProvider.java
@@ -0,0 +1,60 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import javax.swing.Action;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame;
+
+/**
+ * CinemaFramedActionProvider.java
+ *
+ *
+ * Created: Fri Oct 13 17:04:25 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaFramedActionProvider.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface CinemaFramedActionProvider
+{
+ public Action[] getActions( CinemaAlignmentFrame frame );
+}// CinemaFramedActionProvider
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaFramedActionProvider.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/10/19 17:39:12 lord
+ * This provides access to the frame for a module. I am not sure I like
+ * this yet.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.java
new file mode 100644
index 0000000..c0a4126
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaGo.java
@@ -0,0 +1,119 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.cinema.Cinema;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier;
+import uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.apps.optionable.OptionableStateException;
+
+
+/**
+ * CinemaGo.java
+ *
+ * This class actually makes the Cinema gui visible. Effectively its a
+ * dummy module, which I wrote so that I make the gui pop up when it
+ * is fully formed rather than building it whilst its on
+ * screen. Eventually I would like it to do some more things,
+ * particularly provide a progress bar (although I do not know how I
+ * am going to find out what is going on. An event scheme for the
+ * ModuleFactory? How will I know how many modules are going to be loaded?)
+ *
+ * Created: Sat May 27 00:37:17 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGo.java,v 1.7 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaGo extends CinemaGuiModule
+{
+ public void start()
+ {
+ // this sets the size appropriately
+ try{
+ getAlignmentFrame().setOptions();
+ }
+ catch( OptionableStateException ose ){
+ // we should be alright from this, unless its a programming
+ // error!
+ ose.printStackTrace();
+ }
+ catch( Exception exp ){
+ exp.printStackTrace();
+ }
+
+ getFrame().setVisible( true );
+
+ try{
+ // kill the splash screen
+ ((CinemaSplash)Cinema.getSharedModuleInstance( CinemaSharedIdentifier.CINEMA_SPLASH )).killSplash();
+ }
+ catch( ModuleException mde ){
+ // can safely ignore this, as the splash screen is not essential
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaGo.java,v 1.7 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaGo
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGo.java,v $
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/02/19 17:00:32 lord
+ * Added optionability
+ *
+ * Revision 1.5 2001/01/31 17:41:42 lord
+ * Increased robustness
+ *
+ * Revision 1.4 2001/01/27 17:04:02 lord
+ * Removed automatic loading of alignment during load up
+ *
+ * Revision 1.3 2000/12/13 16:28:13 lord
+ * Splash screen support
+ *
+ * Revision 1.2 2000/06/05 14:12:56 lord
+ * Added version method
+ *
+ * Revision 1.1 2000/05/30 16:11:31 lord
+ * Changes due to introduction of CinemaModule.
+ * Added Status bar support
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.java
new file mode 100644
index 0000000..5564c98
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaMenuSystem.java
@@ -0,0 +1,104 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import javax.swing.JMenuBar;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier;
+import uk.ac.man.bioinf.apps.xml.ConfigNode;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaMenuSystem.java
+ *
+ *
+ * Created: Tue May 16 14:24:27 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaMenuSystem.java,v 1.7 2001/05/08 17:39:44 lord Exp $
+ */
+
+public class CinemaMenuSystem extends CinemaGuiModule
+{
+ public void start()
+ {
+ JMenuBar menuBar = getJMenuBar();
+
+ //add the main menu items
+ ConfigNode[] mainMenuItems = getConfigTree().getChildNodes();
+ CinemaMenuBuilder builder = (CinemaMenuBuilder)getRequiredModule( CinemaUtilityIdentifier.CINEMA_MENU_BUILDER );
+ builder.buildMenu( getAlignmentFrame(), menuBar, mainMenuItems );
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaMenuSystem.java,v 1.7 2001/05/08 17:39:44 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaUtilityIdentifier.CINEMA_MENU_BUILDER );
+ return list;
+ }
+
+} // CinemaMenuSystem
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaMenuSystem.java,v $
+ * Revision 1.7 2001/05/08 17:39:44 lord
+ * Cosmetic changes.
+ *
+ * Revision 1.6 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.4 2000/10/19 17:41:08 lord
+ * Most of the code from here has been moved out to the CinemaMenuBuilder
+ *
+ * Revision 1.3 2000/06/27 13:40:26 lord
+ * Changed to reflect method name change in CoreGui
+ *
+ * Revision 1.2 2000/05/30 16:12:32 lord
+ * Changes due to completion of module package.
+ * Changes due to alterations in ConfigNode class producing
+ * better type safety in this class.
+ * Import sorting.
+ *
+ * Revision 1.1 2000/05/18 17:12:19 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.java
new file mode 100644
index 0000000..94c61b1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaModuleCoreIdentifier.java
@@ -0,0 +1,74 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+
+/**
+ * CinemaModuleCoreIdentifer.java
+ *
+ *
+ * Created: Fri May 26 21:39:17 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaModuleCoreIdentifier.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaModuleCoreIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaModuleCoreIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaModuleCoreIdentifier CINEMA_CORE_GUI
+ = new CinemaModuleCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui",
+ "Main GUI frame for cinema" );
+ public static final CinemaModuleCoreIdentifier CINEMA_CORE_VIEW
+ = new CinemaModuleCoreIdentifier( "uk.ac.man.bioinf.apps.cinema.core.CinemaCoreView",
+ "Main view for cinema to provide non Swing specific interface for other modules" );
+} // CinemaModuleCoreIdentifer
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaModuleCoreIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.1 2000/05/30 16:12:47 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.java
new file mode 100644
index 0000000..1995d22
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaSequenceMenu.java
@@ -0,0 +1,110 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import javax.swing.JLabel;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+
+/**
+ * CinemaSequenceMenu.java
+ *
+ *
+ * Created: Mon May 22 14:04:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaSequenceMenu.java,v 1.8 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaSequenceMenu extends CinemaGuiModule
+{
+ private JLabel titleLabel;
+ private GappedSequence currentSequence;
+ private ButtonViewerPopupMenu popupMenu;
+
+ public void start()
+ {
+ popupMenu = new ButtonViewerPopupMenu( getRowHeaders() );
+ popupMenu.add( titleLabel = new JLabel() );
+ }
+
+ public JPopupMenu getPopupMenu()
+ {
+ return popupMenu;
+ }
+
+ public void add( JMenuItem menu )
+ {
+ popupMenu.add( menu );
+ }
+
+ public GappedSequence getLastSequence()
+ {
+ return popupMenu.getSelectedSequence();
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaSequenceMenu.java,v 1.8 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaSequenceMenu
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaSequenceMenu.java,v $
+ * Revision 1.8 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.6 2000/10/19 17:42:07 lord
+ * Moved most of the code out to ButtonViewerPopupMenu
+ *
+ * Revision 1.5 2000/07/18 10:39:38 lord
+ * Import rationalisation.
+ * Changes due to biointerface removal
+ *
+ * Revision 1.4 2000/06/27 13:41:23 lord
+ * Changed popup positioning logic, so that it now works!
+ *
+ * Revision 1.3 2000/06/05 14:13:13 lord
+ * Accessor method for popup menu
+ *
+ * Revision 1.2 2000/05/30 16:13:13 lord
+ * Changes due to completion of module package
+ *
+ * Revision 1.1 2000/05/24 15:36:50 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.java b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.java
new file mode 100644
index 0000000..1efb4ab
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/CinemaSystemEvents.java
@@ -0,0 +1,133 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.systemevents.SystemEventOption;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventProducer;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventSupport;
+import uk.ac.man.bioinf.apps.systemevents.SystemListener;
+import uk.ac.man.bioinf.apps.systemevents.SystemVetoException;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.Module;
+
+
+/**
+ * CinemaSystemEvents.java
+ *
+ *
+ * Created: Thu Apr 20 18:26:56 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaSystemEvents.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaSystemEvents extends Module implements SystemEventProducer
+{
+ SystemEventSupport supp = new SystemEventSupport();
+
+ public void load()
+ {
+ }
+
+ public void start()
+ {
+ }
+
+ public void addSystemEventListener( SystemListener listener )
+ {
+ supp.addSystemEventListener( listener );
+ }
+
+ public void removeSystemEventListener( SystemListener listener )
+ {
+ supp.removeSystemEventListener( listener );
+ }
+
+ public void fireSystemEvent( SystemEventOption option ) throws SystemVetoException
+ {
+ if( Debug.debug )
+ Debug.message( this, "Firing system event " + option );
+ try{
+ supp.fireSystemEvent( option );
+ if( Debug.debug )
+ Debug.message( this, "System event run " );
+ }
+ catch( SystemVetoException sve ){
+ if( Debug.debug )
+ Debug.both( this, "System event exception ", sve );
+ throw sve;
+ }
+ }
+
+ public void fireSystemExit( int i )
+ {
+ try{
+ //Send the event to any listeners
+ //(PENDING) stick up a dialog box here
+ if( Debug.debug )
+ Debug.message( getClass(), "Running system shut down event" );
+ fireSystemEvent( SystemEventOption.SYSTEM_SHUTDOWN );
+ if( Debug.debug )
+ Debug.message( getClass(), "Shutting down system" );
+ System.exit( i );
+ }
+ catch( SystemVetoException exc ){
+ if( Debug.debug )
+ Debug.throwable( getClass(), exc );
+ //No handling is required here. If a listener wants to veto the close
+ //down it should ask the user. Actually this will normally be done as
+ //result of the users reply!
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaSystemEvents.java,v 1.4 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaSystemEvents
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaSystemEvents.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/18 12:10:00 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.2 2000/05/30 16:13:29 lord
+ * Changes due to completion of module package
+ * Import sorting
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.java b/src/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.java
new file mode 100644
index 0000000..8a431cf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/VersionInformation.java
@@ -0,0 +1,166 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core; // Package name inserted by JPack
+import java.net.URL;
+
+
+/**
+ * VersionInformation.java
+ *
+ * This provides standard information about this version of Cinema.
+ *
+ * Created: Wed Apr 19 17:03:28 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: VersionInformation.java,v 1.21 2002/04/20 15:03:42 lord Exp $
+ */
+public class VersionInformation
+{
+ public static String getVersionNumber()
+ {
+ return "3.0.23";
+ }
+
+ public static URL getProjectURL()
+ {
+ return null;
+ }
+
+ public static String getAboutText()
+ {
+ return "Cinema";
+ }
+
+ public static URL[] getAuthorURLs()
+ {
+ return null;
+ }
+
+ public static String getAuthorString()
+ {
+ String[] authString =
+ {
+ "Phillip Lord",
+ "Julian Selley",
+ };
+
+ String retn = "";
+
+ java.util.LinkedList list = new java.util.LinkedList
+ ( java.util.Arrays.asList( authString ) );
+ java.util.Random rand = new java.util.Random();
+
+ while( list.size() > 1 ){
+ int ind = rand.nextInt( list.size() );
+ retn = retn + list.get( ind );
+ if( list.size() != 2 ){
+ retn = retn + ", ";
+ }
+ list.remove( ind );
+ }
+
+ retn = retn + " and " + list.get( 0 );
+ return retn;
+ }
+
+ public static URL getMaintainerURL()
+ {
+ return null;
+ }
+} // VersionInformation
+
+
+
+/*
+ * ChangeLog
+ * $Log: VersionInformation.java,v $
+ * Revision 1.21 2002/04/20 15:03:42 lord
+ * release update
+ *
+ * Revision 1.20 2002/03/19 17:09:48 lord
+ * 3.0.22
+ *
+ * Revision 1.19 2002/03/11 17:35:47 lord
+ * 3.0.21
+ *
+ * Revision 1.18 2002/03/08 14:49:53 lord
+ * Update for 3_0_20
+ *
+ * Revision 1.17 2001/07/10 14:20:01 lord
+ * 3.0.19
+ *
+ * Revision 1.16 2001/07/06 12:39:22 lord
+ * 3.0.18
+ *
+ * Revision 1.15 2001/05/22 15:53:23 lord
+ * Updated to 3.0.17
+ *
+ * Revision 1.14 2001/05/14 17:23:14 lord
+ * Updated for 3.0.16
+ *
+ * Revision 1.13 2001/05/08 17:40:13 lord
+ * Changed for 3.0.15
+ *
+ * Revision 1.12 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.11 2001/04/11 16:30:55 lord
+ * 3.0.14
+ *
+ * Revision 1.10 2001/03/26 15:32:49 lord
+ * Updated for 3.0.12
+ *
+ * Revision 1.9 2001/02/21 15:28:03 lord
+ * Release 3.0.10
+ *
+ * Revision 1.8 2001/02/21 15:15:57 lord
+ * version 3.0.9
+ *
+ * Revision 1.7 2001/01/27 17:13:21 lord
+ * Really updated for 3.0.8
+ *
+ * Revision 1.6 2001/01/27 17:13:00 lord
+ * Update for 3.0.8
+ *
+ * Revision 1.5 2001/01/23 18:03:30 lord
+ * 3.0.7
+ *
+ * Revision 1.4 2001/01/22 13:39:53 lord
+ * Update for 3.0.5
+ *
+ * Revision 1.3 2000/12/05 16:06:17 lord
+ * New version with lots of threading added.
+ *
+ * Revision 1.2 2000/10/12 11:43:13 lord
+ * New version
+ *
+ * Revision 1.1 2000/04/20 16:23:48 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.java b/src/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.java
new file mode 100644
index 0000000..d079abb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestLaunch.java
@@ -0,0 +1,328 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core.test; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.io.File;
+import java.io.FileReader;
+import uk.ac.man.bioinf.apps.cinema.io.ParserFactory;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * CinemaTestLaunch.java
+ *
+ *
+ * Created: Wed Apr 19 18:29:17 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaTestLaunch.java,v 1.11 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaTestLaunch
+{
+
+ private static SequenceAlignment msa;
+
+ public static void main( String[] args ) throws Throwable
+ {
+ try{
+
+ /*
+ CinemaDebug debug = new CinemaDebug();
+ debug.load();
+
+ CinemaSystemEvents event = new CinemaSystemEvents();
+
+ CinemaCoreGui gui = new CinemaCoreGui();
+ gui.load();
+
+ CinemaCoreView view = new CinemaCoreView();
+ view.load();
+ view.start();
+
+ CinemaMenuSystem menu = new CinemaMenuSystem();
+ menu.setCoreGui( gui );
+ menu.load();
+ menu.start();
+
+ CinemaSequenceMenu seqMenu = new CinemaSequenceMenu();
+ seqMenu.setCoreGui( gui );
+ seqMenu.setCoreView( view );
+ seqMenu.load();
+ seqMenu.start();
+
+ CinemaGroupModule grpMod = new CinemaGroupModule();
+ grpMod.setCoreGui( gui );
+ grpMod.setMenuSystem( seqMenu );
+ grpMod.load();
+ grpMod.start();
+
+
+ gui.start();
+ uk.ac.man.bioinf.debug.Debug.throwable( null, new Throwable() );
+ */
+
+ System.out.println( "This class has been throughly nobbled by the introduction of the module architecture" );
+ System.out.println( "I have only failed to remove it because it contains some utility functions which " );
+ System.out.println( "Im still using for the moment" );
+
+ }
+ catch( Throwable thrw ){
+ thrw.printStackTrace();
+ }
+
+
+
+ } //end main method
+
+ public static SequenceAlignment generateMsa() throws Throwable
+ {
+ if( true ){
+ Element[][] elems = new Element[ 6 ][];
+ elems[ 0 ] = AminoAcid.getAll();
+ elems[ 1 ] = AminoAcid.getAll();
+ elems[ 2 ] = AminoAcid.getAll();
+ elems[ 3 ] = AminoAcid.getAll();
+ elems[ 4 ] = AminoAcid.getAll();
+ elems[ 5 ] = AminoAcid.getAll();
+ // elems[ 6 ] = AminoAcid.getAll();
+// elems[ 7 ] = AminoAcid.getAll();
+// elems[ 8 ] = AminoAcid.getAll();
+// elems[ 9 ] = AminoAcid.getAll();
+// elems[ 10 ] = AminoAcid.getAll();
+// elems[ 11 ] = AminoAcid.getAll();
+// elems[ 12 ] = AminoAcid.getAll();
+// elems[ 13 ] = AminoAcid.getAll();
+// elems[ 14 ] = AminoAcid.getAll();
+// elems[ 15 ] = AminoAcid.getAll();
+// elems[ 16 ] = AminoAcid.getAll();
+// elems[ 17 ] = AminoAcid.getAll();
+// elems[ 18 ] = AminoAcid.getAll();
+// elems[ 19 ] = AminoAcid.getAll();
+// elems[ 20 ] = AminoAcid.getAll();
+// elems[ 21 ] = AminoAcid.getAll();
+// elems[ 22 ] = AminoAcid.getAll();
+// elems[ 23 ] = AminoAcid.getAll();
+// elems[ 24 ] = AminoAcid.getAll();
+// elems[ 25 ] = AminoAcid.getAll();
+// elems[ 26 ] = AminoAcid.getAll();
+// elems[ 27 ] = AminoAcid.getAll();
+// elems[ 28 ] = AminoAcid.getAll();
+// elems[ 29 ] = AminoAcid.getAll();
+// elems[ 30 ] = AminoAcid.getAll();
+// elems[ 31 ] = AminoAcid.getAll();
+// elems[ 32 ] = AminoAcid.getAll();
+// elems[ 33 ] = AminoAcid.getAll();
+// elems[ 34 ] = AminoAcid.getAll();
+// elems[ 35 ] = AminoAcid.getAll();
+// elems[ 36 ] = AminoAcid.getAll();
+// elems[ 37 ] = AminoAcid.getAll();
+// elems[ 38 ] = AminoAcid.getAll();
+// elems[ 39 ] = AminoAcid.getAll();
+
+
+ DefaultSequenceAlignment msa = new DefaultSequenceAlignment( elems, ProteinSequenceType.getInstance() );
+ msa.setInset( 3, 13 );
+ msa.setInset( 1, 6 );
+ msa.setInset( 4, 8 );
+ msa.setInset( 2, 4 );
+ msa.setInset( 5, 43 );
+ // msa.setInset( 6, 1 );
+// msa.setInset( 7, 5 );
+// msa.setInset( 8, 0 );
+// msa.setInset( 9, 6 );
+// msa.setInset( 10, 13 );
+// msa.setInset( 13, 3 );
+// msa.setInset( 11, 6 );
+// msa.setInset( 14, 38 );
+// msa.setInset( 12, 4 );
+// msa.setInset( 15, 9 );
+// msa.setInset( 16, 1 );
+// msa.setInset( 17, 5 );
+// msa.setInset( 18, 0 );
+// msa.setInset( 19, 6 );
+// msa.setInset( 20, 3 );
+// msa.setInset( 23, 3 );
+// msa.setInset( 21, 6 );
+// msa.setInset( 24, 8 );
+// msa.setInset( 22, 4 );
+// msa.setInset( 25, 9 );
+// msa.setInset( 26, 1 );
+// msa.setInset( 27, 5 );
+// msa.setInset( 28, 0 );
+// msa.setInset( 29, 6 );
+// msa.setInset( 30, 3 );
+// msa.setInset( 33, 3 );
+// msa.setInset( 31, 6 );
+// msa.setInset( 34, 8 );
+// msa.setInset( 32, 4 );
+// msa.setInset( 35, 9 );
+// msa.setInset( 36, 1 );
+// msa.setInset( 37, 5 );
+// msa.setInset( 38, 0 );
+// msa.setInset( 39, 6 );
+// msa.setInset( 40, 3 );
+
+ return msa;
+ }
+ else{
+
+ /* (PENDING: JNS) 28/07/00 add in ability to get different
+ * parsers (i.e., not just PIR - getAvailableParsers) -
+ * rel. FileSequenceInput
+ */
+ SequenceAlignment seq = (new ParserFactory()).
+ getInputParser("PIR").parse ( new SimpleIdentifier( "GPCRRHODOPSN" ),
+ new FileReader(new File
+ (System.getProperty("user.home") +
+ "/seq/gpcrrhodopsn.seqs" )),
+ new ParserExceptionHandler(){
+ public void handleException( ParserException e )
+ {
+ }
+ });
+
+ return seq;
+ }
+ }
+
+ public static ColorMap generateColorMap()
+ {
+ // color mapping
+ AminoAcid[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if (aa[i] == AminoAcid.GLYCINE)
+ colors[i] = new Color(255, 170, 136);
+ else if (aa[i] == AminoAcid.ALANINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.VALINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.LEUCINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.ISOLEUCINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.SERINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.CYSTEINE)
+ colors[i] = new Color(255, 255, 136);
+ else if (aa[i] == AminoAcid.THREONINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.METHIONINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.PHENYLALANINE)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.TYROSINE)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.TRYPTOPHAN)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.PROLINE)
+ colors[i] = new Color(255, 170, 136);
+ else if (aa[i] == AminoAcid.HISTIDINE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.LYSINE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.ARGININE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.ASPARTICACID)
+ colors[i] = new Color(255, 136, 136);
+ else if (aa[i] == AminoAcid.GLUTAMICACID)
+ colors[i] = new Color(255, 136, 136);
+ else if (aa[i] == AminoAcid.ASPARAGINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.GLUTAMINE)
+ colors[i] = new Color(136, 255, 136);
+ else
+ colors[i] = new Color(102, 102, 102);
+ }
+ colors[ aa.length ] = Color.white;
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ IndividualElementColorMap cm = new IndividualElementColorMap("test", elem, colors);
+ return cm;
+ }
+} // CinemaTestLaunch
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaTestLaunch.java,v $
+ * Revision 1.11 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.10 2000/12/13 16:31:41 lord
+ * Various
+ *
+ * Revision 1.9 2000/08/21 17:20:13 jns
+ * o had to split to input parsers and output parsers - as a result the getParser
+ * changed to getInputParser
+ *
+ * Revision 1.8 2000/08/01 13:28:26 jns
+ * o added in stuff to use parsers rather than original SequenceParser
+ *
+ * Revision 1.7 2000/06/13 11:14:25 lord
+ * Boring changes
+ *
+ * Revision 1.6 2000/05/30 16:13:43 lord
+ * More boring changes
+ *
+ * Revision 1.5 2000/05/24 15:37:07 lord
+ * Added more modules
+ *
+ * Revision 1.4 2000/05/18 17:11:40 lord
+ * To boring to document
+ *
+ * Revision 1.3 2000/05/15 16:22:46 lord
+ * nothing interesting
+ *
+ * Revision 1.1 2000/04/20 16:24:06 lord
+ * Initial checkin
+ *
+ */
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.java b/src/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.java
new file mode 100644
index 0000000..4ce771f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/core/test/CinemaTestModuleLaunch.java
@@ -0,0 +1,82 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.core.test; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.module.DefaultModuleFactoryInstance;
+import uk.ac.man.bioinf.module.Module;
+
+
+/**
+ * CinemaTestModuleLaunch.java
+ *
+ *
+ * Created: Wed May 24 18:37:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaTestModuleLaunch.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaTestModuleLaunch
+{
+ public static void main( String[] args ) throws Throwable
+ {
+ System.out.println( "This class has been nobbled by additions to the module architecture" );
+
+ /*
+ ModuleFactory.setFactoryInstance( new DefaultModuleFactoryInstance() );
+
+ ModuleFactory.addIdentifier
+ ( CinemaCoreIdentifier.CINEMA_CORE_GUI );
+ ModuleFactory.addIdentifier
+ ( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+
+
+ ModuleFactory.load( CinemaCoreIdentifier.CINEMA_CORE_GUI );
+ ModuleFactory.getModule( CinemaCoreIdentifier.CINEMA_CORE_GUI );
+
+ */
+ } //end main method
+} // CinemaTestModuleLaunch
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaTestModuleLaunch.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/13 16:53:02 jns
+ * o bug fix: removal of ModuleFactory class
+ *
+ * Revision 1.1 2000/05/30 16:14:11 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.java b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.java
new file mode 100644
index 0000000..b1fe60d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaAnchorManager.java
@@ -0,0 +1,210 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.group; // Package name inserted by JPack
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import uk.ac.man.bioinf.apps.cinema.CinemaProperties;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceEventType;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+
+
+/**
+ * CinemaAnchorManager.java
+ *
+ * This group takes care of the anchoring groups, and adding and
+ * removing appropriate listeners to the main alignment viewer, and
+ * then adding and removing gaps.
+ *
+ *
+ * Created: Wed Feb 21 18:36:38 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaAnchorManager.java,v 1.3 2001/07/06 11:45:51 lord Exp $
+ */
+
+public class CinemaAnchorManager implements PropertyChangeListener
+{
+
+ // store the listeners in this list.
+ private Map listenerList = new HashMap();
+
+ private CinemaGroupModule module;
+
+ public CinemaAnchorManager( CinemaGroupModule module )
+ {
+ this.module = module;
+ module.addPropertyChangeListener( CinemaProperties.SEQ_ALIGN.toString(), this );
+ }
+
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ // we want to stop listening to all of the groups.
+ if( event.getPropertyName().equals( CinemaProperties.SEQ_ALIGN.toString() ) ){
+ unanchorAll();
+ listenerList.clear();
+ }
+ }
+
+ public void anchorGroup( CinemaGroup group )
+ {
+ if( !listenerList.containsKey( group ) ){
+ AnchorListener listener = new AnchorListener( group );
+ listenerList.put( group, listener );
+ group.addSequenceListener( listener );
+ }
+ }
+
+ public void anchorAll()
+ {
+ CinemaGroup[] group = module.getGroupManager().getAllGroups();
+
+ for( int i = 0; i < group.length; i++ ){
+ anchorGroup( group[ i ] );
+ }
+ }
+
+ public void unanchorGroup( CinemaGroup group )
+ {
+ System.out.println( "Unanchoring group " + group );
+ if( listenerList.containsKey( group ) ){
+ AnchorListener listener = (AnchorListener)listenerList.get( group );
+ listenerList.remove( group );
+ group.removeSequenceListener( listener );
+ }
+ }
+
+ public void unanchorAll()
+ {
+ Iterator iter = listenerList.keySet().iterator();
+ while( iter.hasNext() ){
+ CinemaGroup group = (CinemaGroup)iter.next();
+ AnchorListener listener = (AnchorListener)listenerList.get( group );
+ group.removeSequenceListener( listener );
+ }
+ listenerList.clear();
+ }
+
+ public boolean isAnchored( CinemaGroup group )
+ {
+ return listenerList.containsKey( group );
+ }
+
+ class AnchorListener implements SequenceListener
+ {
+ private SequenceAlignment alignment;
+ // this class actually causes change events to occur, but we want
+ // to ignore them or we will get in to a nasty cycle.
+ private boolean internalChange = false;
+
+ AnchorListener( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ alignment.addSequenceListener( this );
+ }
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ if( !internalChange ){
+ // first we need to calculate the row
+ if( event.getType() == SequenceEventType.GAPINSERT ){
+ int row = alignment.getSequenceIndex( (GappedSequence)event.getSource() );
+
+ int col = event.getStart() +
+ alignment.getInset( row );
+ int numberGaps = event.getLength();
+
+ // now we need to disable this listener or we will get
+ // confused when it adds gaps
+ internalChange = true;
+ for( int i = 1; i < alignment.getNumberSequences() + 1; i++ ){
+ if( i != row ){
+ try{
+ GappedSequence seq = alignment.getSequenceAt( i );
+ seq.insertGapAt( col - alignment.getInset( i ), numberGaps );
+
+ }
+ catch( Exception exp ){
+ exp.printStackTrace();
+ }
+ }
+ }
+ internalChange = false;
+ }else if( event.getType() == SequenceEventType.GAPDELETE ){
+ int row = alignment.getSequenceIndex( (GappedSequence)event.getSource() );
+
+ int col = event.getStart() +
+ alignment.getInset( row );
+ int numberGaps = event.getLength();
+
+ internalChange = true;
+ for( int i = 1; i < alignment.getNumberSequences() + 1; i++ ){
+ if( i != row ){
+ try{
+ GappedSequence seq = alignment.getSequenceAt( i );
+ seq.deleteGapAt( col - alignment.getInset( i ), numberGaps );
+ }
+ catch( NoGapAtThisPositionException ngatpe ){
+ // so there is no gap at this position. So we can't
+ // delete it. So don't
+ }
+ catch( Exception exp ){
+ exp.printStackTrace();
+ }
+ }
+ }
+ internalChange = false;
+ }
+ }
+ }
+ }
+} // CinemaAnchorManager
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaAnchorManager.java,v $
+ * Revision 1.3 2001/07/06 11:45:51 lord
+ * Handling for no gap exceptions
+ *
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/03/12 16:44:19 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.java b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.java
new file mode 100644
index 0000000..293c8ef
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroup.java
@@ -0,0 +1,137 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.group; // Package name inserted by JPack
+import java.awt.Color;
+import java.beans.PropertyChangeEvent;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.group.GroupSequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.AbstractIdentifier;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoSource;
+
+
+
+/**
+ * CinemaGroup.java
+ *
+ * This class is more or less entirely a wrapper around the
+ * HashMap, and just switches all of the return types back to
+ * something sane.
+ * Created: Mon May 22 17:42:36 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGroup.java,v 1.7 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaGroup extends GroupSequenceAlignment
+{
+ private String title;
+ private Color groupColor = Color.black;
+ private CinemaGroupManager manager;
+ private Identifier ident = new CinemaGroupAlignmentIdentifier();
+
+ public CinemaGroup( CinemaGroupManager manager, SequenceAlignment alignment , String title )
+ {
+ super( alignment );
+ this.manager = manager;
+ this.title = title;
+ }
+
+ public String getTitle()
+ {
+ return title;
+ }
+
+ public void setTitle( String title )
+ {
+ String old = this.title;
+ this.title = title;
+
+ manager.firePropertyChange( new PropertyChangeEvent( this, "title", old, title ) );
+ }
+
+ public Color getColor()
+ {
+ return groupColor;
+ }
+
+ public void setColor( Color groupColor )
+ {
+ Color old = groupColor;
+ this.groupColor = groupColor;
+
+ manager.firePropertyChange( new PropertyChangeEvent( this, "color", old, groupColor ) );
+ }
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+
+ class CinemaGroupAlignmentIdentifier extends AbstractIdentifier
+ {
+ CinemaGroupAlignmentIdentifier()
+ {
+ super( new NoSource() );
+ }
+
+ public String getTitle()
+ {
+ return CinemaGroup.this.getTitle();
+ }
+ }
+} // CinemaGroup
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGroup.java,v $
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2000/10/19 17:43:17 lord
+ * Lots of small changes, to extend the functionality.
+ *
+ * Revision 1.5 2000/07/18 10:39:51 lord
+ * Import rationalisation.
+ *
+ * Revision 1.4 2000/06/13 11:14:52 lord
+ * Added some property change support
+ *
+ * Revision 1.3 2000/06/05 14:13:37 lord
+ * Now extends SequenceGroup where most of the logic has gone to
+ *
+ * Revision 1.2 2000/05/30 16:14:28 lord
+ * Added containsSequence method
+ *
+ * Revision 1.1 2000/05/24 15:42:16 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.java b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.java
new file mode 100644
index 0000000..5bda8fa
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupFrame.java
@@ -0,0 +1,487 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ */
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+package uk.ac.man.bioinf.apps.cinema.group; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JFrame;
+import javax.swing.JList;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.border.LineBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.event.MouseInputListener;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensus;
+import uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier;
+import uk.ac.man.bioinf.gui.misc.ChunkyListModel;
+import uk.ac.man.bioinf.gui.misc.SwappingListBasicUI;
+import uk.ac.man.bioinf.gui.optionable.OptionableJFrame;
+import uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+
+
+/**
+
+ * CinemaGroupFrame.java
+ *
+ *
+ * Created: Fri Jun 2 19:19:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGroupFrame.java,v 1.17 2001/07/10 13:40:18 lord Exp $
+
+ */
+
+public class CinemaGroupFrame extends OptionableJFrame
+ implements PropertyChangeListener, ListSelectionListener, ActionListener, AlignmentListener
+{
+ private JList groupsList;
+ private CinemaGroupModule module;
+ private ChunkyListModel groupsListModel, sequencesListModel;
+ private JMenuItem viewGroupAlignment, editGroupName, addToConsensus, createNewGroup,
+ addAllAsGroup, anchor, unanchor, anchorAll, unanchorAll;
+
+ public CinemaGroupFrame( CinemaGroupModule module )
+ {
+ super( "group.cinema.frame", "Cinema Sequence Groups" );
+ this.module = module;
+
+ module.getGroupManager().addPropertyChangeListener( this );
+
+ Container contentPane = getContentPane();
+ OptionableJSplitPane splitPane = new OptionableJSplitPane( "group.cinema.frame.split.pane",
+ JSplitPane.VERTICAL_SPLIT );
+ contentPane.setLayout( new BorderLayout() );
+ contentPane.add( splitPane, BorderLayout.CENTER );
+
+ JPanel topPanel = new JPanel();
+ JPanel bottomPanel = new JPanel();
+
+ // split the frame into two panels
+ topPanel.setBorder( LineBorder.createGrayLineBorder() );
+ bottomPanel.setBorder( LineBorder.createGrayLineBorder() );
+
+ splitPane.setTopComponent( topPanel );
+ splitPane.setBottomComponent( bottomPanel );
+
+
+ // but a scroll pane in the top panel
+ groupsList = new JList( groupsListModel = new ChunkyListModel() );
+ groupsList.setCellRenderer( new GroupListCellRenderer() );
+ groupsList.addListSelectionListener( this );
+ groupsList.setUI( new InformativeSwappingListBasicUI( module ) );
+ topPanel.setLayout( new BorderLayout() );
+ JScrollPane groupListScrollPane = new JScrollPane( groupsList );
+ groupListScrollPane.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Groups" ) );
+ topPanel.add( groupListScrollPane, BorderLayout.CENTER );
+
+
+
+ JList groupMemberList = new JList( sequencesListModel = new ChunkyListModel() );
+ groupMemberList.setCellRenderer( new GroupMemberCellRenderer() );
+ bottomPanel.setLayout( new BorderLayout() );
+ JScrollPane groupMembersListScrollPane = new JScrollPane( groupMemberList );
+ groupMembersListScrollPane.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Group Members" ) );
+ bottomPanel.add( groupMembersListScrollPane, BorderLayout.CENTER );
+
+
+
+ JMenuBar menuBar = new JMenuBar();
+ setJMenuBar( menuBar );
+ JMenu groups = new JMenu( "Group" );
+ menuBar.add( groups );
+
+ editGroupName = new JMenuItem( "Change Group Name" );
+ editGroupName.addActionListener( this );
+ groups.add( editGroupName );
+
+ createNewGroup = new JMenuItem( "Create New Group" );
+ createNewGroup.addActionListener( this );
+ groups.add( createNewGroup );
+
+ addAllAsGroup = new JMenuItem( "Add all sequences as group" );
+ addAllAsGroup.addActionListener( this );
+ groups.add( addAllAsGroup );
+
+ JMenu view = new JMenu( "View" );
+ menuBar.add( view );
+
+ viewGroupAlignment = new JMenuItem( "View Alignment" );
+ viewGroupAlignment.addActionListener( this );
+ view.add( viewGroupAlignment );
+
+ addToConsensus = new JMenuItem( "Add to Consensus Viewer" );
+ addToConsensus.addActionListener( this );
+ view.add( addToConsensus );
+
+ JMenu edit = new JMenu( "Edit" );
+ menuBar.add( edit );
+
+
+ anchor = new JMenuItem( "Anchor group" );
+ anchor.addActionListener( this );
+ edit.add( anchor );
+
+ unanchor = new JMenuItem( "Unanchor group" );
+ unanchor.addActionListener( this );
+ edit.add( unanchor );
+
+ anchorAll = new JMenuItem( "Anchor all" );
+ anchorAll.addActionListener( this );
+ edit.add( anchorAll );
+
+ unanchorAll = new JMenuItem( "Unanchor all" );
+ unanchorAll.addActionListener( this );
+ edit.add( unanchorAll );
+
+ buildGroupsList();
+
+ splitPane.setDefaultDividerLocation( 150 );
+ setDefaultSize( 400, 300 );
+ setVisible( true );
+ }
+
+ /**
+ * Builds the groups list into the Groups List JList
+ */
+ private void buildGroupsList()
+ {
+ groupsListModel.clear();
+ groupsListModel.addAll( module.getGroupManager().getAllGroups() );
+ if( groupsListModel.getSize() == 1 ){
+ groupsList.setSelectedIndex( 0 );
+ }
+ }
+
+ private CinemaGroup getSelectedGroup()
+ {
+ if( groupsList.getSelectedIndex() != - 1 ){
+ return (CinemaGroup)groupsListModel.getElementAt( groupsList.getSelectedIndex() );
+ }
+ return null;
+ }
+
+ // Event listener interfaces....
+ public void actionPerformed( ActionEvent event )
+ {
+ Object src = event.getSource();
+
+ if( src == viewGroupAlignment ){
+ CinemaGroup selected;
+
+ if( (selected = getSelectedGroup()) != null ){
+ CinemaSlaveViewerModule slaveViewerModule
+ = (CinemaSlaveViewerModule)module.getRequiredModule( CinemaUtilityIdentifier.CINEMA_SLAVE_VIEWER );
+ slaveViewerModule.showSlaveAlignment
+ ( selected );
+ }
+ }
+ else if( src == editGroupName ){
+ String newName = JOptionPane.showInputDialog( this, "Please enter the new group name",
+ "New Name", JOptionPane.QUESTION_MESSAGE );
+ if( newName != null ){
+ getSelectedGroup().setTitle( newName );
+ }
+ }
+ else if( src == createNewGroup ){
+ module.getGroupManager().createNewGroup();
+ }
+ else if( src == addToConsensus ){
+ CinemaGroup selected;
+
+ if( (selected = getSelectedGroup()) != null ){
+
+ System.out.println( module.getRequiredModule( CinemaConsensusIdentifier.CINEMA_CONSENSUS ) );
+ System.out.println( ((CinemaConsensus)module.getRequiredModule( CinemaConsensusIdentifier.CINEMA_CONSENSUS )).
+ getDefaultMetaData() );
+
+ System.out.println( ((CinemaConsensus)module.getRequiredModule( CinemaConsensusIdentifier.CINEMA_CONSENSUS )).
+ getDefaultMetaData().getInstance( selected ) );
+
+
+ ConsensusSequence cons =
+ ((CinemaConsensus)module.getRequiredModule( CinemaConsensusIdentifier.CINEMA_CONSENSUS )).
+ getDefaultMetaData().getInstance( selected );
+
+
+ ((CinemaMultipleConsensusViewer)module.getRequiredModule
+ ( CinemaUtilityIdentifier.CINEMA_MULTIPLE_CONSENSUS ))
+ .addConsensusSequence( cons );
+ }
+ }
+ else if( src == addAllAsGroup ){
+ SequenceAlignment align = module.getSequenceAlignment();
+ CinemaGroup group = module.getGroupManager().createNewGroup( "All", getBackground() );
+
+ for( int i = 1; i < (align.getNumberSequences() + 1) ; i ++ ){
+ group.addSequenceToGroup( align.getSequenceAt( i ) );
+ }
+ }
+ else if( src == anchor ){
+ module.getAnchorManager().anchorGroup( getSelectedGroup() );
+ repaint();
+ }
+ else if( src == unanchor ){
+ module.getAnchorManager().unanchorGroup( getSelectedGroup() );
+ repaint();
+ }
+ else if( src == anchorAll ){
+ module.getAnchorManager().anchorAll();
+ repaint();
+ }
+ else if( src == unanchorAll ){
+ module.getAnchorManager().unanchorAll();
+ repaint();
+ }
+ }
+
+ private CinemaGroup lastSelectedGroup;
+
+ public void valueChanged( ListSelectionEvent event )
+ {
+ // single selection so first is the same as the second
+ int index = event.getFirstIndex();
+
+ CinemaGroup selectedGroup = getSelectedGroup();
+ if( selectedGroup == null ) return;
+
+ // ensure that we are only listening to the group that is
+ // currently being displayed
+ if( lastSelectedGroup != null )
+ lastSelectedGroup.removeAlignmentListener( this );
+ selectedGroup.addAlignmentListener( this );
+ lastSelectedGroup = selectedGroup;
+
+ displaySequenceGroup( selectedGroup );
+ }
+
+ private void displaySequenceGroup( CinemaGroup selectedGroup )
+ {
+ // display the newly selected sequence group.
+ sequencesListModel.clear();
+ sequencesListModel.addAll
+ ( selectedGroup.getSequences() );
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ displaySequenceGroup( lastSelectedGroup );
+ }
+
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ if( event.getPropertyName().equals( CinemaGroupManager.groupsName ) ){
+ // if the currently displayed group has been removed, then clear the sequences list.
+ CinemaGroup[] groups = (CinemaGroup[])event.getNewValue();
+ boolean found = false;
+ for( int i = 0; i < groups.length; i++ ){
+ if( groups[ i ] == lastSelectedGroup ){
+ found = true;
+ i = groups.length;
+ }
+ }
+
+ if( !found ) sequencesListModel.clear();
+
+ // then rebuild the group list either way because we know that it has changed.
+ buildGroupsList();
+ }
+
+ if( event.getPropertyName().equals( "title" ) ){
+ buildGroupsList();
+ }
+ }
+
+ class GroupListCellRenderer extends DefaultListCellRenderer
+ {
+ public Component getListCellRendererComponent
+ ( JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus )
+ {
+ CinemaGroup group = (CinemaGroup)value;
+
+ String title = ((module.getAnchorManager().isAnchored( group )) ? "Anc:" : "")
+ + group.getTitle();
+
+ return super.getListCellRendererComponent
+ ( list, title, index, isSelected, cellHasFocus );
+ }
+ }
+
+ class GroupMemberCellRenderer extends DefaultListCellRenderer
+ {
+ public Component getListCellRendererComponent
+ ( JList list, Object value, int index,
+ boolean isSelected, boolean cellHasFocus )
+ {
+ return super.getListCellRendererComponent
+ ( list, ((Sequence)value).getIdentifier().getTitle(), index, isSelected, cellHasFocus );
+ }
+ }
+
+ // the SwappingListBasicUI allows the user to drag the list elements
+ // around. This extension of it traps the swap events, and signals
+ // the CinemaGroupManager that this is being done!
+ class InformativeSwappingListBasicUI extends SwappingListBasicUI
+ {
+ private CinemaGroupManager manager;
+
+ InformativeSwappingListBasicUI( CinemaGroupModule mod )
+ {
+ manager = mod.getGroupManager();
+ }
+
+ protected MouseInputListener createMouseInputListener()
+ {
+ return new InformativeSwappingListHandler();
+ }
+
+ public class InformativeSwappingListHandler extends SwappingMouseInputHandler
+ {
+ protected void swap( int max, int min )
+ {
+
+ // this code is copied directly from that super class, except
+ // for the cast. As far as I can see there is no way of
+ // inheriting this type information, and preventing codeyy
+ // duplication.
+
+ // actually do the swap on the gui
+ JList list = InformativeSwappingListBasicUI.this.getJList();
+
+ ChunkyListModel model = (ChunkyListModel)list.getModel();
+
+ // this lots just swaps the stuff over
+ Object upper = model.remove( max );
+ Object lower = model.getElementAt( min );
+ model.insertElementAt( lower, max );
+ model.remove( min );
+ model.insertElementAt( upper, min );
+
+ //inform the manager
+ manager.swapGroupOrder( max, min );
+ }
+ }
+ }
+
+ public static void main( String[] args )
+ {
+ CinemaGroupFrame frame = new CinemaGroupFrame( null );
+ frame.setVisible( true );
+ frame.pack();
+ frame.repaint();
+ } //end main method
+
+} // CinemaGroupFrame
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGroupFrame.java,v $
+ * Revision 1.17 2001/07/10 13:40:18 lord
+ * Fixed multi alignment viewer bug caused due to method name change
+ *
+ * Revision 1.16 2001/07/06 11:47:17 lord
+ * Ensure one group is always selected
+ *
+ * Revision 1.15 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.14 2001/03/12 16:44:40 lord
+ * Added support for anchoring
+ *
+ * Revision 1.13 2001/02/19 17:00:55 lord
+ * Added optionability
+ *
+ * Revision 1.12 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.11 2000/11/08 18:33:20 lord
+ * Changes to reflect alternation in ConsensusSequence interface
+ *
+ * Revision 1.10 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.9 2000/10/19 17:43:17 lord
+ * Lots of small changes, to extend the functionality.
+ *
+ * Revision 1.8 2000/10/12 11:33:29 lord
+ * Fixed bug with getJList call
+ *
+ * Revision 1.7 2000/10/11 15:41:36 lord
+ * Support for sorting of groups
+ *
+ * Revision 1.6 2000/10/03 17:24:41 lord
+ * Support added for "createNewGroup"
+ *
+ * Revision 1.5 2000/08/01 17:08:53 lord
+ * Now calls the new CinemaConsensus API
+ *
+ * Revision 1.4 2000/07/18 10:40:15 lord
+ * Import rationalisation.
+ * Changes due to removal of biointerface
+ *
+ * Revision 1.3 2000/06/27 13:45:19 lord
+ * Added in multiple consensus viewer logic
+ *
+ * Revision 1.2 2000/06/13 11:16:49 lord
+ * Added Edit Group Name and event handling needed for it.
+ * Added slave alignment viewer
+ *
+ * Revision 1.1 2000/06/05 14:14:43 lord
+ * Initial checkin
+ *
+ */
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.java
new file mode 100644
index 0000000..c104f21
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupIdentifier.java
@@ -0,0 +1,73 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.group; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * CinemaGroupIdentifier.java
+ *
+ *
+ * Created: Thu May 25 18:53:58 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGroupIdentifier.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaGroupIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaGroupIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaGroupIdentifier CINEMA_GROUPS =
+ new CinemaGroupIdentifier( "uk.ac.man.bioinf.apps.cinema.group.CinemaGroupModule", "Cinema Groups systems and associated gui" );
+
+} // CinemaGroupIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGroupIdentifier.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/10/19 17:43:17 lord
+ * Lots of small changes, to extend the functionality.
+ *
+ * Revision 1.2 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.1 2000/05/30 16:14:58 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.java b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.java
new file mode 100644
index 0000000..db81ec2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupManager.java
@@ -0,0 +1,278 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.group; // Package name inserted by JPack
+import java.awt.Color;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import uk.ac.man.bioinf.gui.color.ColorGenerator;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+
+/**
+ * CinemaGroupManager.java
+ *
+ *
+ * Created: Mon May 22 17:36:04 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGroupManager.java,v 1.9 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaGroupManager
+{
+ public static final String groupsName = "groups";
+ public static final String groupsOrder = "order";
+
+ private CinemaGroupModule module;
+ // store the groups
+ private List groups = new LinkedList();
+ private int nextName = 0;
+ private CinemaGroup[] allCache;
+ private boolean allCacheCurrent = false;
+ private ColorGenerator colourGen = ColorGenerator.getLightColorGenerator();
+
+ public CinemaGroupManager( CinemaGroupModule module )
+ {
+ this.module = module;
+ }
+
+ public CinemaGroup[] getAllGroups()
+ {
+ if( !allCacheCurrent ){
+ Object[] retnObj = groups.toArray();
+ allCache = new CinemaGroup[ retnObj.length ];
+ System.arraycopy( retnObj, 0, allCache, 0, retnObj.length );
+ allCacheCurrent = true;
+ }
+ return allCache;
+ }
+
+ /**
+ * Returns group with name or null
+ */
+ public CinemaGroup getGroupByName( String name )
+ {
+ // perhaps need a hash table implementation in here somewhere
+ Iterator iter = groups.iterator();
+
+ while( iter.hasNext() ){
+ CinemaGroup current;
+ if( ( current = (CinemaGroup)iter.next()).getTitle().equals( name ) ){
+ return current;
+ }
+ }
+
+ return null;
+ }
+
+
+ public CinemaGroup createNewGroup( String name, Color colour )
+ {
+ // store the old for the event change
+ CinemaGroup[] old = getAllGroups();
+
+ // create the group
+ CinemaGroup retn = new CinemaGroup( this, module.getSequenceAlignment(), name );
+ retn.setColor( colour );
+ groups.add( retn );
+
+ allCacheCurrent = false;
+
+ module.getAnchorManager().anchorGroup( retn );
+ firePropertyChange( groupsName, old, getAllGroups() );
+ return retn;
+ }
+
+ public CinemaGroup createNewGroup( String name )
+ {
+ return createNewGroup( name, colourGen.next() );
+ }
+
+ public CinemaGroup createNewGroup()
+ {
+ return createNewGroup( "" + (nextName++) );
+ }
+
+ public CinemaGroup getGroupContaining( GappedSequence seq )
+ {
+ Iterator iter = groups.iterator();
+ while( iter.hasNext() ){
+ CinemaGroup retn = (CinemaGroup)iter.next();
+ if( retn.containsSequence( seq ) ) return retn;
+ }
+ return null;
+ }
+
+ public void removeGroup( CinemaGroup group )
+ {
+ if( groups.contains( group ) ){
+ CinemaGroup[] old = getAllGroups();
+ groups.remove( group );
+ allCacheCurrent = false;
+ firePropertyChange( groupsName, old, getAllGroups() );
+ }
+ }
+
+ public void swapGroupOrder( int a, int b )
+ {
+ CinemaGroup[] old = getAllGroups();
+
+ int max = Math.max( a, b );
+ int min = Math.min( a, b );
+
+ // this lots just swaps the stuff over
+ Object upper = groups.remove( max );
+ Object lower = groups.get( min );
+ groups.add( max, lower );
+ groups.remove( min );
+ groups.add( min, upper );
+ allCacheCurrent = false;
+
+ firePropertyChange( groupsOrder, old, getAllGroups() );
+ }
+
+ public void clearGroups()
+ {
+ CinemaGroup[] old = getAllGroups();
+ groups.clear();
+ firePropertyChange( groupsName, old, null );
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaGroupManager.java,v 1.9 2001/04/11 17:04:42 lord Exp $";
+ }
+
+ // property change support
+ // do lazy instantiation. I don't really want to increase the over
+ // head of this class
+ private PropertyChangeSupport supp;
+ public synchronized void addPropertyChangeListener( PropertyChangeListener listener )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.addPropertyChangeListener( listener );
+ }
+
+ public synchronized void removePropertyChangeListener( PropertyChangeListener listener )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.removePropertyChangeListener( listener );
+ }
+
+ public synchronized void addPropertyChangeListener( String propertyName, PropertyChangeListener listener )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.addPropertyChangeListener( propertyName, listener );
+ }
+
+ public synchronized void removePropertyChangeListener
+ ( String propertyName, PropertyChangeListener listener)
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.addPropertyChangeListener( propertyName, listener );
+ }
+
+ protected synchronized void firePropertyChange( String propertyName, Object oldValue, Object newValue )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.firePropertyChange( propertyName, oldValue, newValue );
+ }
+
+ protected synchronized void firePropertyChange( String propertyName, int oldValue, int newValue )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.firePropertyChange( propertyName, oldValue, newValue );
+ }
+
+ protected synchronized void firePropertyChange( PropertyChangeEvent event )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.firePropertyChange( event );
+ }
+
+ public synchronized boolean hasListeners( String propertyName )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ return supp.hasListeners( propertyName );
+ }
+} // CinemaGroupManager
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGroupManager.java,v $
+ * Revision 1.9 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.8 2001/03/12 16:44:57 lord
+ * Added support for anchoring
+ *
+ * Revision 1.7 2000/10/19 17:43:17 lord
+ * Lots of small changes, to extend the functionality.
+ *
+ * Revision 1.6 2000/10/11 15:41:36 lord
+ * Support for sorting of groups
+ *
+ * Revision 1.5 2000/07/18 10:41:06 lord
+ * Added some convenience methods
+ *
+ * Revision 1.4 2000/06/13 11:17:18 lord
+ * Changes to reflect alterations in CinemaGroup
+ *
+ * Revision 1.3 2000/06/05 14:14:31 lord
+ * Substantial rewrite of class
+ *
+ * Revision 1.2 2000/05/30 16:15:27 lord
+ * Added getGroupContaining method
+ *
+ * Revision 1.1 2000/05/24 15:42:16 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.java b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.java
new file mode 100644
index 0000000..690cdb3
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/group/CinemaGroupModule.java
@@ -0,0 +1,387 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+
+package uk.ac.man.bioinf.apps.cinema.group; // Package name inserted by JPack
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.CinemaProperties;
+import uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaSequenceMenu;
+import uk.ac.man.bioinf.apps.cinema.group.CinemaGroupFrame;
+import uk.ac.man.bioinf.apps.cinema.group.CinemaGroupManager;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+
+
+/**
+ * CinemaGroupModule.java
+ *
+ *
+ * Created: Tue May 23 15:42:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaGroupModule.java,v 1.15 2001/04/11 17:04:42 lord Exp $
+ */
+public class CinemaGroupModule extends CinemaModule
+ implements ActionListener, CinemaActionProvider, PropertyChangeListener, AlignmentListener
+{
+ private JMenuItem createNewGroup, removeFromGroup;
+ private JMenu deleteGroup, addToGroup;
+
+ private CinemaGroupManager groups;
+ private CinemaSequenceMenu seqMenu;
+ private CinemaGroupFrame groupDialog;
+ private CinemaAnchorManager anchor;
+
+
+ public void load()
+ {
+ groups = new CinemaGroupManager( this );
+ groups.addPropertyChangeListener( this );
+ anchor = new CinemaAnchorManager( this );
+ }
+
+ public void start()
+ {
+ seqMenu = getMenuSystem();
+
+ createNewGroup = new JMenuItem( "Create New Group" );
+ createNewGroup.addActionListener( this );
+ seqMenu.add( createNewGroup );
+
+ deleteGroup = new JMenu( "Delete Group" );
+
+ addToGroup = new JMenu( "Add to Group" );
+
+ removeFromGroup = new JMenuItem( "Remove From Group" );
+ removeFromGroup.addActionListener( this );
+
+ regenerateGroupMenu( groups.getAllGroups() );
+ seqMenu.getPopupMenu().addSeparator();
+ addCinemaPropertyChangeListener( CinemaProperties.SEQ_ALIGN.toString(), this );
+ }
+
+ public GappedSequence getLastSequence()
+ {
+ return getMenuSystem().getLastSequence();
+ }
+
+ public CinemaAnchorManager getAnchorManager()
+ {
+ return anchor;
+ }
+
+ public CinemaGroupManager getGroupManager()
+ {
+ return groups;
+ }
+
+ private boolean groupMenusPresent = false;
+
+ private void regenerateGroupMenu( CinemaGroup[] cinemaGroups )
+ {
+ if( cinemaGroups.length > 0 ){
+ if( !groupMenusPresent ){
+ int i;
+
+ for( i = 0; i < seqMenu.getPopupMenu().getComponentCount(); i++ ){
+ if( seqMenu.getPopupMenu().getComponent( i ) == createNewGroup ) break;
+ } //end for( i < seqMenu.getComponentCount() )
+
+ i++;
+ seqMenu.getPopupMenu().add( removeFromGroup, i );
+ seqMenu.getPopupMenu().add( addToGroup, i );
+ seqMenu.getPopupMenu().add( deleteGroup, i );
+ groupMenusPresent = true;
+ }
+
+ deleteGroup.removeAll();
+ addToGroup.removeAll();
+
+ for( int i = 0; i< cinemaGroups.length; i++ ){
+ // put the menu item for the delete group
+ JMenuItem delGroup = new JMenuItem( cinemaGroups[ i ].getTitle() );
+ deleteGroup.add( delGroup );
+ delGroup.addActionListener( new DeleteGroupActionListener( cinemaGroups[ i ] ) );
+
+ // put the menu item for the add to group
+ JMenuItem addGroup = new JMenuItem( cinemaGroups[ i ].getTitle() );
+ addToGroup.add( addGroup );
+ addGroup.addActionListener( new AddToGroup( cinemaGroups[ i ] ) );
+ }
+ }
+ else{
+ // there are no cinema groups, therefore remove the delete, add, and remove from group buttons.
+ seqMenu.getPopupMenu().remove( removeFromGroup );
+ seqMenu.getPopupMenu().remove( addToGroup );
+ seqMenu.getPopupMenu().remove( deleteGroup );
+ groupMenusPresent = false;
+ }
+ }
+
+ class DeleteGroupActionListener implements ActionListener
+ {
+ private CinemaGroup group;
+
+ DeleteGroupActionListener( CinemaGroup group )
+ {
+ this.group = group;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ int retVal = JOptionPane.showConfirmDialog
+ ( null, "Do you really want to delete group \"" + group.getTitle() + "\"",
+ "Delete Group", JOptionPane.YES_NO_OPTION );
+
+ if( retVal == JOptionPane.OK_OPTION ){
+ GappedSequence[] seqs = group.getGappedSequences();
+
+ for( int i = 0; i < seqs.length; i++ ){
+ clearSequenceTitleColor( seqs[ i ] );
+ }
+ groups.removeGroup( group );
+ }
+ }
+ }
+
+ class AddToGroup implements ActionListener
+ {
+ private CinemaGroup group;
+
+ AddToGroup( CinemaGroup group )
+ {
+ this.group = group;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ GappedSequence seq = getLastSequence();
+ group.addSequenceToGroup( seq );
+ setSequenceTitleColor( seq, group.getColor() );
+ }
+ }
+
+ private CinemaSequenceMenu menuSystem;
+ public CinemaSequenceMenu getMenuSystem()
+ {
+ if( menuSystem == null ){
+ menuSystem = (CinemaSequenceMenu)getRequiredModule( CinemaCoreIdentifier.CINEMA_SEQUENCE_MENU );
+ }
+ return menuSystem;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ Object source = event.getSource();
+
+ if( source == createNewGroup ){
+ // (PENDING:- PL) Need a dialog box which returns a name I think
+ groups.createNewGroup();
+ }
+
+ if( source == removeFromGroup ){
+ GappedSequence seq = getLastSequence();
+ CinemaGroup group = groups.getGroupContaining( seq );
+ if( group != null ){
+ group.removeSequenceFromGroup( seq );
+ clearSequenceTitleColor( seq );
+ }
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaGroupModule.java,v 1.15 2001/04/11 17:04:42 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaCoreIdentifier.CINEMA_SEQUENCE_MENU );
+ list.add( CinemaUtilityIdentifier.CINEMA_SLAVE_VIEWER );
+ list.add( CinemaConsensusIdentifier.CINEMA_CONSENSUS );
+ list.add( CinemaUtilityIdentifier.CINEMA_MULTIPLE_CONSENSUS );
+ return list;
+ }
+
+ // forwards groups events
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ // (PENDING:- PL) This needs to be altered to switch a boolean,
+ // which can regenerate the group menu when it is needed, rather
+ // than automatically....
+ if( event.getPropertyName().equals( CinemaGroupManager.groupsName ) ){
+ // we need to ensure that we are listening only to current
+ // groups.
+
+ // remove this as a listener
+ CinemaGroup[] oldGroups = (CinemaGroup[])event.getOldValue();
+ for( int i = 0; i < oldGroups.length; i++ ){
+ oldGroups[ i ].removeAlignmentListener( this );
+ }
+
+ CinemaGroup[] newGroups = groups.getAllGroups();
+ for( int i = 0; i < newGroups.length; i++ ){
+ newGroups[ i ].addAlignmentListener( this );
+ }
+
+ // and regenerate the group menu so that it is correct also.
+ regenerateGroupMenu( groups.getAllGroups() );
+ }
+
+ if( event.getPropertyName().equals( CinemaProperties.SEQ_ALIGN.toString() ) ){
+ // remove all the groups as they are all going to be wrong.
+ CinemaGroup[] allGroups = groups.getAllGroups();
+
+ for( int i = 0; i < allGroups.length; i++ ){
+ groups.removeGroup( allGroups[ i ] );
+ }
+
+ regenerateGroupMenu( groups.getAllGroups() );
+ }
+
+ if( event.getPropertyName().equals( "title" ) ){
+ regenerateGroupMenu( groups.getAllGroups() );
+ }
+
+ if( event.getPropertyName().equals( CinemaGroupManager.groupsOrder ) ){
+ regenerateGroupMenu( groups.getAllGroups() );
+ }
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ // it will be a CinemaGroup that has caused this alignment event.
+ CinemaGroup group = (CinemaGroup)event.getSource();
+ Color col = group.getColor();
+
+ if( event.getType() == AlignmentEventType.INSERT ){
+ for( int i = event.getStart(); i < event.getEnd() + 1; i++ ){
+ setSequenceTitleColor( group.getSequenceAt( i ), col );
+ }
+ }
+
+ if( event.getType() == AlignmentEventType.DELETE ){
+ for( int i = event.getStart(); i < event.getEnd() + 1; i++ ){
+ clearSequenceTitleColor( group.getSequenceAt( i ) );
+ }
+ }
+ }
+
+ public Action[] getActions()
+ {
+ Action[] retn = new Action[ 1 ];
+ retn[ 0 ] = new AbstractAction( "Group Editor" ){
+ public void actionPerformed( ActionEvent event )
+ {
+ if( groupDialog == null ){
+ groupDialog = new CinemaGroupFrame( CinemaGroupModule.this );
+ }
+ groupDialog.setVisible( true );
+ }
+ };
+ return retn;
+ }
+} // CinemaGroupModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaGroupModule.java,v $
+ * Revision 1.15 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.14 2001/03/12 16:45:04 lord
+ * Added support for anchoring
+ *
+ * Revision 1.13 2000/11/10 15:12:32 lord
+ * CinemaMultipleConsensus re-enabled
+ *
+ * Revision 1.12 2000/11/09 16:42:13 lord
+ * Package update
+ *
+ * Revision 1.11 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.10 2000/10/19 17:43:17 lord
+ * Lots of small changes, to extend the functionality.
+ *
+ * Revision 1.9 2000/10/11 15:41:36 lord
+ * Support for sorting of groups
+ *
+ * Revision 1.8 2000/10/03 17:12:58 lord
+ * Confirm dialog on delete group added
+ *
+ * Revision 1.7 2000/08/01 17:09:15 lord
+ * Now requires CinemaConsensus
+ *
+ * Revision 1.6 2000/07/18 11:00:34 lord
+ * Updated listener and event handling. Now ceases to listen to an
+ * Group once it has been removed from the Manager
+ *
+ * Revision 1.5 2000/06/27 15:54:35 lord
+ * Now requires Consensus Module
+ *
+ * Revision 1.4 2000/06/13 11:17:41 lord
+ * Now listens for changes in titles
+ *
+ * Revision 1.3 2000/06/05 14:17:15 lord
+ * Now checks to see whether there are any groups before adding menu
+ * items.
+ * Implemented ActionProvider interface.
+ * Added support for CinemaGroupFrame popup
+ *
+ * Revision 1.2 2000/05/30 16:16:20 lord
+ * Mostly changes due to module architecture completion
+ *
+ * Revision 1.1 2000/05/24 15:42:16 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.java b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.java
new file mode 100644
index 0000000..34ce45b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInput.java
@@ -0,0 +1,284 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import java.awt.event.ActionEvent;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JOptionPane;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.io.AlignmentInputParser;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+
+
+/**
+ * This class is abstract and will be extended by any sequence input
+ * modules. It merely provides the action stuff for the menu system,
+ * and describes an abstract method run by the actionPerformed(...)
+ * and implemented by the children of this class.
+ *
+ *
+ * Created: Wed Jun 14 15:26:56 2000
+ *
+ * @author Julian Selley
+ * @version $Id: AbstractSequenceInput.java,v 1.13 2002/04/20 14:59:05 lord Exp $
+ */
+
+public abstract class AbstractSequenceInput extends CinemaGuiModule
+ implements CinemaActionProvider
+{
+ private static final Map parserMap = new HashMap();
+ protected AbstractSequenceParserExceptionHandler eh;
+
+ public final String[] getAvailableParsers()
+ {
+ Object[] keys = ((Set)parserMap.keySet()).toArray();
+ String[] retn = new String[ keys.length ];
+
+ System.arraycopy( keys, 0, retn, 0, keys.length );
+ return retn;
+ }
+
+ public final AlignmentInputParser getParser( String keyOfParser )
+ {
+ AlignmentInputParser retn = null;
+
+ try{
+ retn = (AlignmentInputParser)
+ (((Class)parserMap.get( keyOfParser)).newInstance());
+ }
+ catch( InstantiationException ie ){
+ if( Debug.debug )
+ Debug.both( this, "Input Parser Error", ie );
+ }
+ catch( IllegalAccessException iae ){
+ if( Debug.debug )
+ Debug.both( this, "Input Parser Error", iae );
+ }
+
+ return retn;
+ }
+
+ public final String getParserDescription( String keyOfParser )
+ {
+ return getParser( keyOfParser ).getDescription();
+ }
+
+ public void load() throws ModuleException
+ {
+ Properties configProps = getConfigProperties();
+
+ for ( Enumeration e = configProps.propertyNames() ; e.hasMoreElements() ;){
+ try{
+ String parserKey = (String)e.nextElement();
+ if( !parserKey.equals( "default" ) ){
+ String parserClassName = configProps.getProperty( parserKey );
+ parserClassName = parserClassName.substring( 4, parserClassName.length() );
+ Class parserClass = getClass().getClassLoader().
+ loadClass( parserClassName );
+
+ parserMap.put( parserKey, parserClass );
+ }
+ }
+ catch( ClassNotFoundException cnfe ){
+ if( Debug.debug )
+ cnfe.printStackTrace();
+ throw new ModuleException( cnfe );
+ }
+ }
+ }
+
+ /**
+ * Supplies the action for the menu system/whatever else wishes to
+ * invoke this modules action.
+ *
+ * @return the possible actions
+ */
+ public Action[] getActions()
+ {
+ Action[] rtn = new Action[1];
+
+ rtn[0] = new AbstractAction("Open...") {
+ public void actionPerformed(ActionEvent event)
+ {
+ SequenceAlignment alignment = openAlignment();
+
+ setSequenceAlignment( alignment );
+
+ // if there are parser exceptions ask whether to display them
+ if (eh != null) {
+ ParserException[] parserExceptions = eh.getParserExceptions();
+ if (parserExceptions.length != 0 ) {
+ if( parserExceptions.length < 10 ){
+ JOptionPane message = new JOptionPane();
+ int status = message.showConfirmDialog
+ (getFrame(),
+ "Sequence errors were detected in parsing, but were dealt with \n" +
+ "by putting a gap in the offending position\n" +
+ "Do you wish to see the errors?\n",
+ "Warning: Sequence errors",
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.WARNING_MESSAGE);
+ // if selected yes, then display the errors in a
+ // separate dialog
+ if (status == JOptionPane.YES_OPTION) {
+ // put exceptions into one stringbuffer
+ StringBuffer exceptionStringBuffer = new StringBuffer();
+ for (int i = 0; i < parserExceptions.length; i++) {
+ exceptionStringBuffer.append
+ (parserExceptions[i].getIdentifier().getTitle() + ": " +
+ parserExceptions[i].getMessage() + "\n");
+ }
+ // display the errors
+ JOptionPane errors = new JOptionPane();
+ errors.showMessageDialog
+ (getFrame(),
+ "The errors were: \n" + exceptionStringBuffer.toString(),
+ "Sequence errors",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ else{
+ JOptionPane message = new JOptionPane();
+ message.showMessageDialog
+ ( getFrame(),
+ "Sequence errors were detected in parsing. These\n" +
+ "have been replaced by gaps. However there were a\n" +
+ "large number so you may be using an unsupported format\n",
+ "Warning: Sequence errors",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ }
+ }
+ };
+
+ return rtn;
+ }
+
+ /**
+ * Obtains the sequence alignment by the relevent method.
+ *
+ * @return the sequence alignment
+ */
+ public abstract SequenceAlignment openAlignment();
+
+
+ /**
+ * Sets the parser exception handler.
+ *
+ * @param eh exception handler
+ */
+ public void setExceptionHandler
+ (AbstractSequenceParserExceptionHandler exceptionHandler)
+ {
+ eh = exceptionHandler;
+ }
+
+ /**
+ * Returns the parser exception handler.
+ *
+ * @return the exception handler
+ */
+ public ParserExceptionHandler getExceptionHandler()
+ {
+ return eh;
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ return super.getRequiredIdentifiers();
+ }
+} // AbstractSequenceInput
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequenceInput.java,v $
+ * Revision 1.13 2002/04/20 14:59:05 lord
+ * Improved error handling
+ *
+ * Revision 1.12 2001/07/06 12:38:49 lord
+ * Removed debug output
+ *
+ * Revision 1.11 2001/05/29 13:01:15 lord
+ * Filled in method
+ *
+ * Revision 1.10 2001/05/24 15:38:57 lord
+ * Parsers are now configurable. Added save as option.
+ *
+ * Revision 1.9 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.8 2001/01/27 16:53:41 lord
+ * Removed status information, as this is done seperately now.
+ *
+ * Revision 1.7 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.6 2000/10/13 14:32:54 jns
+ * o sorting out a problem with null elements (X) that I had previously
+ * had working, but I then messed it up trying to be smart. I have sorted
+ * by taking out the actualy formation of the sequence, but supplied the
+ * basic elements for creating the sequence.
+ *
+ * Revision 1.5 2000/09/11 13:20:08 lord
+ * Puts alignment source or identifier in the window frame now.
+ *
+ * Revision 1.4 2000/08/21 17:18:55 jns
+ * o input parser exception handler changed to just one exception handler - there
+ * dont need to be two
+ * o changed menu item name to open rather than open alignment
+ *
+ * Revision 1.3 2000/08/01 14:53:06 jns
+ * o change of name of ParseException ParserException
+ *
+ * Revision 1.2 2000/06/29 16:10:33 jns
+ * o added error code handling
+ * o changed exception handler type
+ *
+ * Revision 1.1 2000/06/16 09:41:55 jns
+ * o initial code for a sequence input modules, inc. for the moment just the
+ * file sequence input module.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.java b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.java
new file mode 100644
index 0000000..6190f3b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceInputParserExceptionHandler.java
@@ -0,0 +1,103 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import java.util.ArrayList;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+
+
+/**
+ * AbstractSequenceInputParserExceptionHandler provides methods so
+ * that the exceptions can be stored and at a later date shown all
+ * together. This is the intended methodology to be used for Cinema.
+ *
+ *
+ * Created: Fri Jun 16 14:06:51 2000
+ *
+ * @author Julian Selley
+ * @version $Id: AbstractSequenceInputParserExceptionHandler.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class AbstractSequenceInputParserExceptionHandler
+ implements ParserExceptionHandler
+{
+ private ArrayList parserExceptions = new ArrayList();
+
+ /**
+ * Stores the exception, so that later a call can be made to
+ * getParserExceptions() in order to display all the exceptions
+ * together. The normal exception handler will just store the
+ * exception and allow a gap to be inserted in the sequence.
+ *
+ * @param e the parser exception
+ */
+ public void storeException(ParserException e)
+ {
+ this.parserExceptions.add(e);
+ }
+
+ /**
+ * Return the stored exceptions, so that they can be displayed all
+ * together.
+ *
+ * @return the exceptions
+ */
+ public ParserException[] getParserExceptions()
+ {
+ Object[] exceptions = this.parserExceptions.toArray();
+ ParserException[] rtn = new ParserException[exceptions.length];
+
+ System.arraycopy(exceptions, 0, rtn, 0, exceptions.length);
+ return rtn;
+ }
+
+ /**
+ * Clears all exceptions that have been stored.
+ */
+ public void clearExceptions()
+ {
+ this.parserExceptions.clear();
+ }
+} // AbstractSequenceInputParserExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequenceInputParserExceptionHandler.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/08/01 14:54:10 jns
+ * o change of name from ParseException to ParserException - more logical
+ *
+ * Revision 1.1 2000/06/30 09:36:42 jns
+ * o added so that exceptions may be stored for printing at a later stage
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.java b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.java
new file mode 100644
index 0000000..853bd50
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceOutput.java
@@ -0,0 +1,188 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import java.awt.event.ActionEvent;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.io.AlignmentOutputParser;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * This class is abstract and will be extended by any sequence output
+ * modules. It merely provides the action stuff for the menu system,
+ * and describes an abstract method run by the actionPerformed(...)
+ * and implemented by the children of this class.
+ *
+ *
+ * Created: Mon Jul 31 22:22:33 2000
+ *
+ * @author Julian Selley
+ * @version $Id: AbstractSequenceOutput.java,v 1.5 2001/07/06 11:48:08 lord Exp $
+ */
+
+public abstract class AbstractSequenceOutput extends CinemaGuiModule
+ implements CinemaActionProvider
+{
+ private static final Map parserMap = new HashMap();
+ protected AbstractSequenceParserExceptionHandler eh;
+
+ public final String[] getAvailableParsers()
+ {
+ Object[] keys = ((Set)parserMap.keySet()).toArray();
+ String[] retn = new String[ keys.length ];
+
+ System.arraycopy( keys, 0, retn, 0, keys.length );
+ return retn;
+ }
+
+ public final AlignmentOutputParser getParser( String keyOfParser )
+ {
+ AlignmentOutputParser retn = null;
+
+ try{
+ retn = (AlignmentOutputParser)
+ (((Class)parserMap.get( keyOfParser )).newInstance());
+ }
+ catch( InstantiationException ie ){
+ if( Debug.debug )
+ Debug.both( this, "Input Parser Error", ie );
+ }
+ catch( IllegalAccessException iae ){
+ if( Debug.debug )
+ Debug.both( this, "Input Parser Error", iae );
+ }
+
+ return retn;
+ }
+
+ public void load() throws ModuleException
+ {
+ Properties configProps = getConfigProperties();
+
+ for ( Enumeration e = configProps.propertyNames() ; e.hasMoreElements() ;){
+ try{
+ String parserKey = (String)e.nextElement();
+ if( !parserKey.equals( "default" ) ){
+ String parserClassName = configProps.getProperty( parserKey );
+ parserClassName = parserClassName.substring( 4, parserClassName.length() );
+ Class parserClass = getClass().getClassLoader().
+ loadClass( parserClassName );
+
+ parserMap.put( parserKey, parserClass );
+ }
+ }
+ catch( ClassNotFoundException cnfe ){
+ if( Debug.debug )
+ cnfe.printStackTrace();
+ throw new ModuleException( cnfe );
+ }
+ }
+ }
+
+ public final String getParserDescription( String keyOfParser )
+ {
+ return getParser( keyOfParser ).getDescription();
+ }
+
+
+ public Action[] getActions()
+ {
+ Action[] rtn = new Action[ 2 ];
+
+ rtn[0] = new AbstractAction("Save...") {
+ public void actionPerformed(ActionEvent event)
+ {
+ saveAlignment(getSequenceAlignment());
+ }
+ };
+
+ rtn[ 1 ] = new AbstractAction( "Save as..." ){
+ public void actionPerformed( ActionEvent event )
+ {
+ saveAlignmentAs( getSequenceAlignment() );
+ }
+ };
+ return rtn;
+ }
+
+ public abstract void saveAlignment(SequenceAlignment sa);
+
+ public abstract void saveAlignmentAs( SequenceAlignment sa );
+
+
+ public void setExceptionHandler
+ (AbstractSequenceParserExceptionHandler exceptionHandler)
+ {
+ eh = exceptionHandler;
+ }
+
+ public ParserExceptionHandler getExceptionHandler()
+ {
+ return eh;
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ return super.getRequiredIdentifiers();
+ }
+} // AbstractSequenceOutput
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequenceOutput.java,v $
+ * Revision 1.5 2001/07/06 11:48:08 lord
+ * Removed debug
+ *
+ * Revision 1.4 2001/05/29 13:01:31 lord
+ * Removed ParserFactory
+ *
+ * Revision 1.3 2001/05/24 15:38:57 lord
+ * Parsers are now configurable. Added save as option.
+ *
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.java b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.java
new file mode 100644
index 0000000..bd485cb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/AbstractSequenceParserExceptionHandler.java
@@ -0,0 +1,106 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import java.util.ArrayList;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+
+
+/**
+ * AbstractSequenceInputParserExceptionHandler provides methods so
+ * that the exceptions can be stored and at a later date shown all
+ * together. This is the intended methodology to be used for Cinema.
+ *
+ *
+ * Created: Fri Jun 16 14:06:51 2000
+ *
+ * @author Julian Selley
+ * @version $Id: AbstractSequenceParserExceptionHandler.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class AbstractSequenceParserExceptionHandler
+ implements ParserExceptionHandler
+{
+ private ArrayList parserExceptions = new ArrayList();
+
+ /**
+ * Stores the exception, so that later a call can be made to
+ * getParserExceptions() in order to display all the exceptions
+ * together. The normal exception handler will just store the
+ * exception and allow a gap to be inserted in the sequence.
+ *
+ * @param e the parser exception
+ */
+ public void storeException(ParserException e)
+ {
+ this.parserExceptions.add(e);
+ }
+
+ /**
+ * Return the stored exceptions, so that they can be displayed all
+ * together.
+ *
+ * @return the exceptions
+ */
+ public ParserException[] getParserExceptions()
+ {
+ Object[] exceptions = this.parserExceptions.toArray();
+ ParserException[] rtn = new ParserException[exceptions.length];
+
+ System.arraycopy(exceptions, 0, rtn, 0, exceptions.length);
+ return rtn;
+ }
+
+ /**
+ * Clears all exceptions that have been stored.
+ */
+ public void clearExceptions()
+ {
+ this.parserExceptions.clear();
+ }
+} // AbstractSequenceParserExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequenceParserExceptionHandler.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ * Revision 1.2 2000/08/01 14:54:10 jns
+ * o change of name from ParseException to ParserException - more logical
+ *
+ * Revision 1.1 2000/06/30 09:36:42 jns
+ * o added so that exceptions may be stored for printing at a later stage
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.java b/src/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.java
new file mode 100644
index 0000000..b1327df
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParser.java
@@ -0,0 +1,204 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import gnu.getopt.Getopt;
+import gnu.getopt.LongOpt;
+import java.io.File;
+import java.io.IOException;
+import uk.ac.man.bioinf.apps.cinema.Cinema;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.sequence.identifier.FileSource;
+import uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier;
+
+
+/**
+ * CinemaCommandLineParser.java
+ *
+ * This module is responsible for parsing the command line to Cinema
+ * and invoking what ever actions are necessary.
+ * <p>
+ * <b>(PENDING: JNS)</b> 28-11-00 currently this is all hard coded and will
+ * need to be altered and recompiled each time the command line
+ * options are changed.
+ * <p>
+ *
+ * Created: Mon Nov 27 17:36:39 2000
+ *
+ * @author Julian Selley
+ * @version $Id: CinemaCommandLineParser.java,v 1.7 2001/05/24 15:39:13 lord Exp $
+ */
+
+public class CinemaCommandLineParser extends CinemaModule
+{
+ private String[] cmdLn; // the command line as supplied to cinema
+ private Getopt cmdLnOpts; // the getopt object for the command line
+
+ public CinemaCommandLineParser() {}
+
+ public void load() throws ModuleException
+ {
+ // store the command line for use later
+ cmdLn = Cinema.getCommandLineArguments();
+
+ /* get the command line arguments from and create the Getopt
+ * object
+ */
+ cmdLnOpts = new Getopt("cinema", // program name
+ cmdLn, // command line args
+ // the getopt syntax for what to expect
+ /* -i: in file
+ * -p: parser
+ */
+ "-:i:p:L:U:C:V:D:",
+ // a set of longopts
+ new LongOpt[] {
+ /* --in: in file - rel. to -i
+ */
+ new LongOpt("in", LongOpt.REQUIRED_ARGUMENT,
+ null, 'i'),
+ /* --parser: parser to use
+ */
+ new LongOpt("parser", LongOpt.REQUIRED_ARGUMENT,
+ null, 'p')
+ });
+
+ }
+
+ public void start()
+ {
+ int c;
+ boolean filenameSet = false;
+ String filename = null;
+ String parser = "PIR";
+
+ // while there are options
+ while ((c = cmdLnOpts.getopt()) != -1)
+ switch (c) {
+ // in file option
+ case 'i':
+ filename = cmdLnOpts.getOptarg();
+ filenameSet = true;
+ break;
+ case 'p':
+ parser = cmdLnOpts.getOptarg();
+ break;
+ }
+
+ // if no option tag was supplied
+ if ( !filenameSet && (cmdLnOpts.getOptind() <= cmdLn.length) && ( cmdLn.length > 0 ))
+ filename = cmdLn[cmdLnOpts.getOptind() - 1];
+
+ // if the filename has been declared, load the file
+ if (filename != null)
+ openFile(filename, parser);
+ }
+
+ /**
+ * Opens a declared file in Cinema.
+ *
+ * @param filename the filename
+ * @param parser the parser to use
+ */
+ public void openFile(String filename, String parser)
+ {
+ try {
+ // create a file object using the filename
+ File file = new File(filename);
+ // determine the header to use for the SimpleIdentifier
+ // there is logic behind this - I want just the name, ex. the
+ // pathname
+ String fileNameNoExtension = file.getName();
+ int i = fileNameNoExtension.lastIndexOf('.');
+ if (i > 0 && i < fileNameNoExtension.length() - 1)
+ fileNameNoExtension = fileNameNoExtension.substring(0, i);
+ fileNameNoExtension = fileNameNoExtension.toUpperCase();
+
+ // get file module
+ FileSequenceInput fsim = (FileSequenceInput)getContext().getModule
+ (SequenceInputModuleIdentifier.FILE_INPUT);
+
+ // open the file and set the alignment
+ setSequenceAlignment
+ (fsim.openFile
+ (new File(filename),
+ fsim.getParser(parser),
+ new SimpleIdentifier(fileNameNoExtension, new FileSource(file))));
+ } catch (ModuleException e) {
+ /* (PENDING: JNS) 20.12.00 May need to deal with this
+ * properly. Needs more thought than a simple debug statement.
+ */
+ Debug.both(this, "File Sequence Input Module not found!", e);
+ } catch (IOException e) {
+ Debug.both(this, "File was not found!", e);
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaCommandLineParser.java,v 1.7 2001/05/24 15:39:13 lord Exp $";
+ }
+} // CinemaCommandLineParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaCommandLineParser.java,v $
+ * Revision 1.7 2001/05/24 15:39:13 lord
+ * Modified due to changes in Input module
+ *
+ * Revision 1.6 2001/05/04 12:30:33 lord
+ * Cosmetic changes
+ *
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2001/03/12 16:45:18 lord
+ * Added some more options
+ *
+ * Revision 1.3 2001/01/31 17:42:07 lord
+ * Removed interface identifier reference
+ *
+ * Revision 1.2 2001/01/15 18:52:19 lord
+ * Cosmetic changes.
+ * Improved exception handling.
+ * Bug fix, in case of no command line options
+ *
+ * Revision 1.1 2001/01/04 12:57:30 jns
+ * o CINEMA command line processor. Code will be improved to look at an
+ * XML file and from there load relevent code. Currently the code simply
+ * loads a file from the command line, and has the option for a parser to
+ * be specified. -i <filename> or <filename> to simply load a file. The
+ * PIR parser is currently used by default (there are no other parsers as
+ * yet).
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.java
new file mode 100644
index 0000000..f225249
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/CinemaCommandLineParserIdentifier.java
@@ -0,0 +1,73 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * The identifier for the CinemaCommandLineParser module.
+ *
+ *
+ * Created: Thu Dec 21 12:34:24 2000
+ *
+ * @author Julian Selley
+ * @version $Id: CinemaCommandLineParserIdentifier.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaCommandLineParserIdentifier
+ extends AbstractEnumeratedModuleIdentifier
+{
+ private CinemaCommandLineParserIdentifier(String className, String toString)
+ {
+ super(className, toString);
+ }
+
+ public static final CinemaCommandLineParserIdentifier COMMAND_LINE_PARSER =
+ new CinemaCommandLineParserIdentifier
+ ("uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParser",
+ "Provides the command line parsing module");
+} // CinemaCommandLineParserIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaCommandLineParserIdentifier.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/04 12:57:30 jns
+ * o CINEMA command line processor. Code will be improved to look at an
+ * XML file and from there load relevent code. Currently the code simply
+ * loads a file from the command line, and has the option for a parser to
+ * be specified. -i <filename> or <filename> to simply load a file. The
+ * PIR parser is currently used by default (there are no other parsers as
+ * yet).
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.java b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.java
new file mode 100644
index 0000000..abf5b9d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInput.java
@@ -0,0 +1,238 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.io.AlignmentInputParser;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.FileSource;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier;
+
+
+/**
+ * FileSequenceInput is a that module covers sequence input into
+ * Cinema via files. It extends the abstract sequence input module
+ * which provides the basics of any sequence input method into
+ * Cinema. It is currently Cinema only the abstract sequence input
+ * module extends the Cinema GUI module.
+ *
+ *
+ * Created: Thu Jun 15 15:07:12 2000
+ *
+ * @author Julian Selley
+ * @version $Id: FileSequenceInput.java,v 1.15 2002/04/20 14:58:56 lord Exp $
+ */
+
+public class FileSequenceInput extends AbstractSequenceInput
+{
+ private JFileChooser chooser = new JFileChooser();
+ private String defaultParser;
+
+ public FileSequenceInput()
+ {
+ super.setExceptionHandler(new FileSequenceParserExceptionHandler());
+ }
+
+ public void start()
+ {
+ super.start();
+
+ // fetch the default parser from the config information.
+ defaultParser = getConfigProperties().getProperty( "default" );
+ defaultParser = defaultParser.substring( 4, defaultParser.length() );
+ }
+
+
+ /**
+ * Opens a file using a parser. This method was generated to allow
+ * file parsing without the need for the open dialog - i.e., it will
+ * make the passing of arguments to Cinema of the file name a lot
+ * easier, or even possible.
+ * @param file the file
+ * @param parser the input parser
+ * @param ident the identifier for the alignment
+ * @return the sequence alignment
+ */
+ public SequenceAlignment openFile(File file, AlignmentInputParser parser,
+ Identifier ident)
+ throws IOException
+ {
+ return parser.parse(ident, new FileReader(file), getExceptionHandler());
+ }
+
+ public SequenceAlignment openAlignment()
+ {
+ SequenceAlignment alignment = null;
+
+ /* (PENDING: JNS 14/06/00)
+ * x obtain list of parsers from ParserFactory
+ * o set potential file types
+ * x open file browser
+ * x get file
+ * x pass file + file type (& therefore parser) -> ParserFactory
+ * x return alignment
+ */
+
+ // obtain a list of the parsers from the factory
+ String[] availableParsers = getAvailableParsers();
+
+ // (PENDING: JNS 15/06/00) set the file types from the parsers
+ //for (int i = 0; i < availableParsers.length; i++) {
+ // chooser.addChoosableFileFilter();
+ //}
+
+ // open the file chooser
+ int selected = chooser.showOpenDialog(getFrame());
+ // if open a file then pass it to the parse factory
+ if (selected == JFileChooser.APPROVE_OPTION) {
+ File file;
+ if ( (file = chooser.getSelectedFile()) != null)
+ try {
+ // get alignment through parsing file
+ /* (PENDING: JNS 15/06/00) change "PIR" to something dynamic
+ * - will come with the writing of getting the parsers and
+ * getting the choosen parser
+ */
+
+ // calculate the identifier based on the File name without extension
+ String fileName = file.getName();
+ int i = fileName.lastIndexOf( '.' );
+ String fileNameNoExtension = fileName;
+ if( i > 0 && i < fileName.length() - 1 ){
+ fileNameNoExtension = fileName.substring( 0, i );
+ }
+ fileNameNoExtension = fileNameNoExtension.toUpperCase();
+
+ // open the file and get the alignment
+ alignment = openFile(file, getParser( defaultParser ),
+ new SimpleIdentifier(fileNameNoExtension,
+ new FileSource(file)));
+
+ } catch (IOException e) {
+ if (e instanceof FileNotFoundException) {
+ if (Debug.debug)
+ Debug.message(this, "File Sequence Input: File not found");
+ JOptionPane message = new JOptionPane();
+ message.showMessageDialog
+ (getFrame(),
+ "The file doesn't exist! Please choose again",
+ "ERROR: File not found",
+ JOptionPane.ERROR_MESSAGE);
+ alignment = openAlignment();
+ } else if (Debug.debug)
+ Debug.both(this, "File Seuqence Input: An IOException was found",
+ e);
+ }
+ }
+
+ if( alignment.getNumberSequences() == 0 ){
+ JOptionPane message = new JOptionPane();
+ message.showMessageDialog
+ (getFrame(),
+ "The file is either empty, or in an unsupported format. Please Choose again",
+ "ERROR: Empty file, or unknown format",
+ JOptionPane.ERROR_MESSAGE);
+ alignment = openAlignment();
+ }
+
+ // return the alignment
+ return alignment;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: FileSequenceInput.java,v 1.15 2002/04/20 14:58:56 lord Exp $";
+ }
+} // FileSequenceInput
+
+
+
+/*
+ * ChangeLog
+ * $Log: FileSequenceInput.java,v $
+ * Revision 1.15 2002/04/20 14:58:56 lord
+ * Improved error handling
+ *
+ * Revision 1.14 2001/05/24 15:39:29 lord
+ * Modified due to changes in parser factory
+ *
+ * Revision 1.13 2001/05/08 17:40:31 lord
+ * Default parser now configurable
+ *
+ * Revision 1.12 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.11 2001/04/11 16:31:20 lord
+ * Changed default to seqret. Need to parameterise this class
+ *
+ * Revision 1.10 2001/01/27 16:54:03 lord
+ * Removed status information which was not working anyway
+ *
+ * Revision 1.9 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.8 2000/11/13 16:55:25 jns
+ * o split of openAlignment into gui stuff and opening the file. This
+ * will help later when doing command line loading which previously would
+ * not have been possible. Not sure this is the best implementation, it
+ * may be changed at a later stage to be incorperated in the interface.
+ *
+ * Revision 1.7 2000/10/31 15:51:55 lord
+ * Added support for SequenceIdentifiers. Needs to be improved though.
+ *
+ * Revision 1.6 2000/09/11 16:23:41 lord
+ * Put in new status message
+ *
+ * Revision 1.5 2000/09/11 13:20:08 lord
+ * Puts alignment source or identifier in the window frame now.
+ *
+ * Revision 1.4 2000/08/21 17:23:24 jns
+ * o reverting to standard exception handlers - no need for input and output
+ * distinctions
+ * o things specific to input parsers - name changes basically
+ *
+ * Revision 1.3 2000/08/01 14:55:18 jns
+ * o AlignmentParser to AlignmentInputParser change of name so that output
+ * parsers can be plugged in more logically.
+ *
+ * Revision 1.2 2000/06/30 09:55:09 jns
+ * o added in 'file not found' handling
+ * o some pendings still outstanding.
+ *
+ * Revision 1.1 2000/06/16 09:41:55 jns
+ * o initial code for a sequence input modules, inc. for the moment just the
+ * file sequence input module.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.java b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.java
new file mode 100644
index 0000000..14f0c9b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceInputParserExceptionHandler.java
@@ -0,0 +1,76 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.io.ParserException;
+
+
+/**
+ * FileSequenceInputParserExceptionHandler handles parser exceptions
+ * to do with parsing files, and will display a dialog box.
+ *
+ *
+ * Created: Thu Jun 15 23:39:37 2000
+ *
+ * @author Julian Selley
+ * @version $Id: FileSequenceInputParserExceptionHandler.java,v 1.5 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class FileSequenceInputParserExceptionHandler
+ extends AbstractSequenceInputParserExceptionHandler
+{
+ public FileSequenceInputParserExceptionHandler() {}
+
+ public void handleException(ParserException e)
+ {
+ storeException(e);
+ }
+} // FileSequenceInputParserExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: FileSequenceInputParserExceptionHandler.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/08/01 14:56:01 jns
+ * o ParseException to ParserException to be more logical and avoid confusion
+ *
+ * Revision 1.2 2000/06/30 09:33:24 jns
+ * o now stores exception for printing at a later stage
+ *
+ * Revision 1.1 2000/06/16 09:41:55 jns
+ * o initial code for a sequence input modules, inc. for the moment just the
+ * file sequence input module.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.java b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.java
new file mode 100644
index 0000000..60b6b00
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceOutput.java
@@ -0,0 +1,167 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.FileSource;
+import uk.ac.man.bioinf.sequence.identifier.Source;
+
+
+/**
+ * FileSequenceOutput is a module that covers sequence output to a
+ * file from Cinema. It extends the abstract sequence output module
+ * that provides the basics of any sequence output from Cinema.
+ *
+ *
+ * Created: Mon Jul 31 22:18:18 2000
+ *
+ * @author Julian Selley
+ * @version $Id: FileSequenceOutput.java,v 1.7 2001/05/29 13:01:31 lord Exp $
+ */
+
+public class FileSequenceOutput extends AbstractSequenceOutput
+{
+ JFileChooser chooser = new JFileChooser();
+
+ public FileSequenceOutput()
+ {
+ super.setExceptionHandler(new FileSequenceParserExceptionHandler());
+ }
+
+ public void saveAlignment( SequenceAlignment sa )
+ {
+ Source source = sa.getIdentifier().getSource();
+
+ // check whether there is a file associated with this sequence
+ // alignment. If no then we need to find out what the file should
+ // be from the user.
+ if( !( source instanceof FileSource ) ){
+ saveAlignmentAs( sa );
+ return;
+ }
+
+
+ FileSource fileSource = (FileSource)source;
+
+ try {
+ FileWriter writer = new FileWriter( fileSource.getFile() );
+
+ super.getParser("PIR").write
+ (sa, writer, getExceptionHandler());
+
+ // flush the writer and close it
+ writer.flush();
+ writer.close();
+ } catch (IOException e) {
+ JOptionPane.showMessageDialog
+ ( null, "<html>There was a problem with saving the results: <p>" +
+ e.getMessage(), "Warning", JOptionPane.ERROR_MESSAGE );
+
+ if (Debug.debug)
+ Debug.both(this, "File Sequence Output: An IOException was found",
+ e);
+ }
+ }
+
+ public void saveAlignmentAs(SequenceAlignment sa)
+ {
+ String[] availableParsers = super.
+ getAvailableParsers();
+
+ // (PENDING: JNS 01/08/00) set the file types from the parsers
+ //for (int i = 0; i < availableParsers.length; i++) {
+ // chooser.addChoosableFileFilter();
+ //}
+
+ // open the file chooser
+ int selected = chooser.showSaveDialog(getFrame());
+ // if save a file then pass it to the parse factory
+ if (selected == JFileChooser.APPROVE_OPTION) {
+ File selectedFile;
+ if ( (selectedFile = chooser.getSelectedFile()) != null) {
+
+ if( selectedFile.exists() ){
+ Object[] options = { "OK", "CANCEL" };
+ int retn = JOptionPane.showOptionDialog
+ (null, "<html>This file already exists.<p> "
+ + "Are you sure you want to overwrite it. <p>", "Warning",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ if( retn == 1 ) return;
+ }
+
+ FileSource fileSource = new FileSource
+ ( chooser.getSelectedFile() );
+
+ sa.getIdentifier().setSource( fileSource );
+ saveAlignment( sa );
+ }
+ }
+ }
+
+
+ public String getVersion()
+ {
+ return "$Id: FileSequenceOutput.java,v 1.7 2001/05/29 13:01:31 lord Exp $";
+ }
+} // FileSequenceOutput
+
+
+
+/*
+ * ChangeLog
+ * $Log: FileSequenceOutput.java,v $
+ * Revision 1.7 2001/05/29 13:01:31 lord
+ * Removed ParserFactory
+ *
+ * Revision 1.6 2001/05/24 16:01:47 lord
+ * Now put in error handling that actually works.
+ *
+ * Revision 1.5 2001/05/24 15:41:28 lord
+ * Improved error handling.
+ *
+ * Revision 1.4 2001/05/24 15:39:29 lord
+ * Modified due to changes in parser factory
+ *
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/20 15:58:45 jns
+ * o bug-fix: writer needed flushing and closing in order for all the
+ * information to be written to file.
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.java b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.java
new file mode 100644
index 0000000..e20978a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/FileSequenceParserExceptionHandler.java
@@ -0,0 +1,79 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.io.ParserException;
+
+
+/**
+ * FileSequenceParserExceptionHandler handles parser exceptions
+ * to do with parsing files, and will display a dialog box.
+ *
+ *
+ * Created: Thu Jun 15 23:39:37 2000
+ *
+ * @author Julian Selley
+ * @version $Id: FileSequenceParserExceptionHandler.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class FileSequenceParserExceptionHandler
+ extends AbstractSequenceParserExceptionHandler
+{
+ public FileSequenceParserExceptionHandler() {}
+
+ public void handleException(ParserException e)
+ {
+ storeException(e);
+ }
+} // FileSequenceParserExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: FileSequenceParserExceptionHandler.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/10/19 17:43:37 lord
+ * Import rationalisation.
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ * Revision 1.3 2000/08/01 14:56:01 jns
+ * o ParseException to ParserException to be more logical and avoid confusion
+ *
+ * Revision 1.2 2000/06/30 09:33:24 jns
+ * o now stores exception for printing at a later stage
+ *
+ * Revision 1.1 2000/06/16 09:41:55 jns
+ * o initial code for a sequence input modules, inc. for the moment just the
+ * file sequence input module.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.java
new file mode 100644
index 0000000..0d0ba53
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/SequenceInputModuleIdentifier.java
@@ -0,0 +1,84 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * A module interface identifier for sequence input. It will deligate
+ * to the different protocols available (e.g: file input, http
+ * input).
+ *
+ *
+ * Created: Tue Jun 13 12:43:25 2000
+ *
+ * @author Julian Selley
+ * @version $Id: SequenceInputModuleIdentifier.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class SequenceInputModuleIdentifier
+ extends AbstractEnumeratedModuleIdentifier
+{
+ private SequenceInputModuleIdentifier( String className, String toString, boolean isInterface )
+ {
+ super( className, toString, isInterface );
+ }
+
+ public static final SequenceInputModuleIdentifier SEQ_INPUT =
+ new SequenceInputModuleIdentifier( "uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceInput",
+ "Provides the interface for Sequence input into cinema",
+ true );
+ public static final SequenceInputModuleIdentifier FILE_INPUT =
+ new SequenceInputModuleIdentifier( "uk.ac.man.bioinf.apps.cinema.io.FileSequenceInput",
+ "Provides input from a file into cinema",
+ false );
+} // SequenceInputModuleIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceInputModuleIdentifier.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/31 17:43:59 lord
+ * Created after removing InterfaceIdentifier
+ *
+ * Revision 1.3 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/08/03 16:41:29 lord
+ * Now have this working correctly as an interface module
+ *
+ * Revision 1.1 2000/06/16 09:41:55 jns
+ * o initial code for a sequence input modules, inc. for the moment just the
+ * file sequence input module.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.java
new file mode 100644
index 0000000..c10c919
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/io/SequenceOutputModuleIdentifier.java
@@ -0,0 +1,78 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * SequenceOutputModuleIdentifier.java
+ *
+ *
+ * Created: Fri Aug 11 15:06:07 2000
+ *
+ * @author Julian Selley
+ * @version $Id: SequenceOutputModuleIdentifier.java,v 1.3 2001/05/29 13:01:31 lord Exp $
+ */
+
+public class SequenceOutputModuleIdentifier
+ extends AbstractEnumeratedModuleIdentifier
+{
+ private SequenceOutputModuleIdentifier(String className, String toString, boolean isInterface)
+ {
+ super(className, toString, isInterface);
+ }
+
+ public static final SequenceOutputModuleIdentifier SEQ_OUTPUT =
+ new SequenceOutputModuleIdentifier("uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput",
+ "Provides output from cinema into file",
+ true);
+ public static final SequenceOutputModuleIdentifier FILE_OUTPUT =
+ new SequenceOutputModuleIdentifier("uk.ac.man.bioinf.apps.cinema.io.FileSequenceOutput",
+ "Provides output from cinema into file",
+ false);
+} // SequenceOutputModuleIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceOutputModuleIdentifier.java,v $
+ * Revision 1.3 2001/05/29 13:01:31 lord
+ * Removed ParserFactory
+ *
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/31 17:43:59 lord
+ * Created after removing InterfaceIdentifier
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.java b/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.java
new file mode 100644
index 0000000..d10a6ea
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifFrame.java
@@ -0,0 +1,748 @@
+
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.motif; // Package name inserted by JPack
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.io.Writer;
+import java.util.Iterator;
+import javax.swing.BoxLayout;
+import javax.swing.ButtonGroup;
+import javax.swing.DefaultListModel;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+import javax.swing.ListSelectionModel;
+import javax.swing.border.LineBorder;
+import javax.swing.border.TitledBorder;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import uk.ac.man.bioinf.apps.cinema.CinemaProperties;
+import uk.ac.man.bioinf.apps.cinema.io.AbstractSequenceOutput;
+import uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier;
+import uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier;
+import uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+import uk.ac.man.bioinf.io.AlignmentOutputParser;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.util.Direction;
+
+
+
+/**
+ * CinemaMotifFrame.java
+ *
+ *
+ * Created: Tue Jan 16 13:54:41 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaMotifFrame.java,v 1.12 2001/07/10 14:15:24 lord Exp $
+ */
+
+public class CinemaMotifFrame extends JFrame
+ implements ActionListener, AlignmentSelectionListener, ListSelectionListener, PropertyChangeListener
+{
+ private JList selectionList, sequencesList;
+ private DefaultListModel selectionListModel, sequencesListModel;
+ private JButton plusNorth, plusEast, plusSouth, plusWest;
+ private JButton minusNorth, minusEast, minusSouth, minusWest, quit;
+ private JButton clearAll, clearSelected, saveSelected, save;
+ private JCheckBox sortMotifs;
+ private JTextField motifName, selectionRegion;
+ private TitledBorder motifNameBorder;
+ private NamedAlignmentSelectionModel model;
+ private CinemaMotifModule module;
+
+
+ public CinemaMotifFrame( NamedAlignmentSelectionModel model, CinemaMotifModule module )
+ {
+ super( "Cinema Motif Manager" );
+ this.setDefaultCloseOperation( HIDE_ON_CLOSE );
+
+ // top level panels. All expansion goes to the list
+ Container contentPane = getContentPane();
+
+ JPanel topPanel = new JPanel();
+ JPanel bottomPanel = new JPanel();
+
+ topPanel.setBorder( LineBorder.createGrayLineBorder() );
+ bottomPanel.setBorder( LineBorder.createGrayLineBorder() );
+ contentPane.setLayout( new BorderLayout() );
+ contentPane.add( topPanel, BorderLayout.CENTER );
+ contentPane.add( bottomPanel, BorderLayout.SOUTH );
+
+ // now define the top panel
+ // first we do the region JList with scroll and border
+ selectionList = new JList( selectionListModel = new DefaultListModel() );
+ selectionList.addListSelectionListener( this );
+ topPanel.setLayout( new BorderLayout() );
+ JScrollPane listScrollPane = new JScrollPane( selectionList );
+ listScrollPane.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Motifs" ) );
+ topPanel.add( listScrollPane, BorderLayout.CENTER );
+
+ // now the button panel
+ // we want to seperate the close button from the rest if possible
+ JPanel buttonAndQuit = new JPanel();
+ buttonAndQuit.setLayout( new BorderLayout() );
+ quit = new JButton( "Close" );
+ quit.addActionListener( this );
+ buttonAndQuit.add( quit, BorderLayout.SOUTH );
+
+ JPanel buttonPanel = new JPanel();
+ buttonPanel.setLayout( new BoxLayout( buttonPanel, BoxLayout.Y_AXIS ) );
+ buttonAndQuit.add( buttonPanel, BorderLayout.CENTER );
+
+ topPanel.add( buttonAndQuit, BorderLayout.EAST );
+
+
+ clearAll = new JButton( "Clear All Motifs" );
+ clearAll.addActionListener( this );
+ buttonPanel.add( clearAll );
+
+ clearSelected = new JButton( "Clear Selected Motifs" );
+ clearSelected.addActionListener( this );
+ buttonPanel.add( clearSelected );
+
+ save = new JButton( "Save motifs" );
+ save.addActionListener( this );
+ buttonPanel.add( save );
+
+ saveSelected = new JButton( "Save selected motif" );
+ saveSelected.addActionListener( this );
+ buttonPanel.add( saveSelected );
+
+ // sort motifs is a toggle. The default state is set below, after
+ // more initialisation.
+ sortMotifs = new JCheckBox( "Sort Motifs" );
+ sortMotifs.addActionListener( this );
+ buttonPanel.add( sortMotifs );
+
+
+ // bottom panel
+ JPanel infoPanel = new JPanel();
+ JPanel sizePanel = new JPanel();
+ bottomPanel.setLayout( new BorderLayout() );
+
+ bottomPanel.add( infoPanel, BorderLayout.CENTER );
+ bottomPanel.add( sizePanel, BorderLayout.EAST );
+
+ // the size panel manually increases or decreases the size of the selection
+ sizePanel.setLayout( new GridLayout( 0, 1 ) );
+
+ JPanel increaseSize = new JPanel();
+ increaseSize.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Increase Size" ) );
+ increaseSize.setLayout( new BorderLayout() );
+
+ plusNorth = new JButton( "+" );
+ plusNorth.addActionListener( this );
+ increaseSize.add( plusNorth, BorderLayout.NORTH );
+
+ plusEast = new JButton( "+" );
+ plusEast.addActionListener( this );
+ increaseSize.add( plusEast, BorderLayout.EAST );
+
+ plusSouth = new JButton( "+" );
+ plusSouth.addActionListener( this );
+ increaseSize.add( plusSouth, BorderLayout.SOUTH );
+
+ plusWest = new JButton( "+" );
+ plusWest.addActionListener( this );
+ increaseSize.add( plusWest, BorderLayout.WEST );
+
+ sizePanel.add( increaseSize );
+
+ JPanel decreaseSize = new JPanel();
+ decreaseSize.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Decrease Size" ) );
+ decreaseSize.setLayout( new BorderLayout() );
+
+ minusNorth = new JButton( "-" );
+ minusNorth.addActionListener( this );
+ decreaseSize.add( minusNorth, BorderLayout.NORTH );
+
+ minusEast = new JButton( "-" );
+ minusEast.addActionListener( this );
+ decreaseSize.add( minusEast, BorderLayout.EAST );
+
+ minusSouth = new JButton( "-" );
+ minusSouth.addActionListener( this );
+ decreaseSize.add( minusSouth, BorderLayout.SOUTH );
+
+ minusWest = new JButton( "-" );
+ minusWest.addActionListener( this );
+ decreaseSize.add( minusWest, BorderLayout.WEST );
+
+ sizePanel.add( decreaseSize );
+
+
+ // the information panel prints (and allows editing of) information.
+ infoPanel.setLayout( new BoxLayout( infoPanel, BoxLayout.Y_AXIS ) );
+ infoPanel.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Motif Information" ) );
+
+ // the motif name. The editable status of this is set below, when
+ // the auto sort status default is set.
+ motifName = new JTextField();
+ motifName.addActionListener( this );
+ motifName.setBorder
+ ( motifNameBorder = new TitledBorder( LineBorder.createGrayLineBorder(), "" ) );
+ infoPanel.add( motifName );
+
+ JList sequencesList = new JList( sequencesListModel = new DefaultListModel() );
+ sequencesList.addListSelectionListener( this );
+ sequencesList.setSelectionMode( ListSelectionModel.SINGLE_SELECTION );
+
+ JScrollPane sequencesListScroll = new JScrollPane( sequencesList );
+ sequencesListScroll.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Sequences" ) );
+ infoPanel.add( sequencesListScroll );
+
+ selectionRegion = new JTextField();
+ selectionRegion.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Motifs" ) );
+ infoPanel.add( selectionRegion );
+
+ //diagnostic color scheme
+ //topPanel.setBackground( Color.red );
+ // bottomPanel.setBackground( Color.green );
+ // listScrollPane.setBackground( Color.orange );
+ // buttonAndQuit.setBackground( Color.cyan );
+ // buttonPanel.setBackground( Color.blue );
+ // infoPanel.setBackground( Color.cyan );
+ // sizePanel.setBackground( Color.pink );
+ // increaseSize.setBackground( Color.magenta );
+ // decreaseSize.setBackground( Color.yellow );
+
+ // store the model and install listeners
+ this.model = model;
+ this.module = module;
+ model.addAlignmentSelectionListener( this );
+
+
+ module.addCinemaPropertyChangeListener
+ ( CinemaProperties.SEQ_ALIGN.toString(), this );
+
+ // switch the motif auto sorter to its default value. This also
+ // affects these gui components.
+ setSortMotif( true );
+
+ pack();
+ }
+
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ // we are only listening to sequence alignment changes
+ clearAllSelections();
+ }
+
+ private void fillGuiFromModel()
+ {
+ Iterator iter = model.getSelectionNameIterator();
+
+ while( iter.hasNext() ){
+ selectionListModel.addElement( iter.next() );
+ }
+ ensureOneSelection();
+ }
+
+ private void ensureOneSelection()
+ {
+ // if we have just added the first one then we want to ensure
+ // that is selected. This makes it a little more obvious what is
+ // going on.
+
+ if( selectionListModel.getSize() > 0
+ && selectionList.getSelectedIndex() == - 1 ){
+ selectionList.setSelectedIndex( 0 );
+ }
+ }
+
+
+ private void setSortMotif( boolean sortP )
+ {
+ if( sortP ){
+ sortMotifs.setSelected( true );
+ motifName.setEditable( false );
+ motifNameBorder.setTitle( "Motif Name" );
+ sortMotifs();
+ }
+ else{
+ sortMotifs.setSelected( false );
+ motifName.setEditable( true );
+ motifNameBorder.setTitle( "Motif Name (Return to set)" );
+ }
+ }
+
+ private void sortMotifs()
+ {
+ // first we want to sort the motifs
+ model.sortMotifs();
+
+ // now update the gui
+ int selected = getCurrentlySelectedIndex();
+ selectionListModel.removeAllElements();
+ fillGuiFromModel();
+ selectionList.setSelectedIndex( selected );
+
+
+ // and now rename everything appropriately
+ String name = module.getSequenceAlignment().getIdentifier().getTitle();
+
+ for( int i = 0; i < selectionListModel.size(); i++ ){
+ String currentName = (String) selectionListModel.getElementAt( i );
+
+ System.out.println( "Setting " + currentName + " to " + (name + (i + 1) + "_1") );
+
+ setNameAt
+ ( currentName, name + (i + 1) + "_1", i );
+ }
+ }
+
+ public boolean isCurrentlySelected()
+ {
+ return ( getCurrentlySelectedIndex() != -1 );
+ }
+
+ public int getCurrentlySelectedIndex()
+ {
+ return selectionList.getSelectedIndex();
+ }
+
+ public String getCurrentlySelectedName()
+ {
+ if( !isCurrentlySelected() ) return null;
+ return (String)selectionListModel.getElementAt
+ ( getCurrentlySelectedIndex() );
+ }
+
+ public SequenceAlignmentRectangle getCurrentlySelectedRect()
+ {
+ if( !isCurrentlySelected() ) return null;
+ return model.getSelectionForName( getCurrentlySelectedName() );
+ }
+
+ private AbstractSequenceOutput abst;
+ private ParserExceptionHandler exceptionHandler;
+
+
+ // save all motifs. The File here is the directory.
+ private void saveMotif( File file, String format )
+ {
+ for( int i = 0; i < selectionListModel.size(); i++ ){
+ String motifName = (String)selectionListModel.getElementAt( i );
+ saveMotif( new File( file, motifName + "." + format.toLowerCase() ), motifName,
+ format );
+ }
+ }
+
+ // save the selected motif, in the specified File
+ private void saveMotif( File file, String name, String format )
+ {
+ try{
+ // we need to get hold of the parsers first
+ if( abst == null ){
+ abst = (AbstractSequenceOutput)module.getRequiredModule
+ ( SequenceOutputModuleIdentifier.FILE_OUTPUT );
+
+ exceptionHandler = abst.getExceptionHandler();
+ }
+
+ AlignmentOutputParser out = abst.getParser( format );
+
+ // now fetch the sequence alignment
+ SequenceAlignmentRectangle rect = model.getSelectionForName( name );
+ SequenceAlignment mainAlignment = module.getSequenceAlignment();
+
+ SequenceAlignment motif = mainAlignment.getSubAlignment( rect );
+
+ Writer write;
+
+ out.write
+ ( motif, write = new BufferedWriter
+ ( new OutputStreamWriter( new FileOutputStream( file ) ) ), exceptionHandler );
+
+ write.close();
+ }
+ catch( IOException iop ){
+ JOptionPane.showMessageDialog
+ ( null, "<html>There was a problem with saving the results: <p>" +
+ iop.getMessage(), "Warning", JOptionPane.ERROR_MESSAGE );
+
+ }
+ }
+
+ public void valueChanged( ListSelectionEvent event )
+ {
+ if( event.getSource() == selectionList ){
+ updateGuiForSelection();
+ }
+ }
+
+ private void updateGuiForSelection()
+ {
+ if( isCurrentlySelected() ){
+
+ String selectionName = getCurrentlySelectedName();
+
+ // update the gui
+ motifName.setText( selectionName );
+
+ // update the sequences list
+ sequencesListModel.clear();
+
+ SequenceAlignmentRectangle rect = getCurrentlySelectedRect();
+ SequenceAlignment alignment = module.getSequenceAlignment();
+
+ try{
+ for( int i = rect.getY(); i < rect.getY() + rect.getHeight(); i++ ){
+ sequencesListModel.addElement( alignment.getSequenceAt( i ).getIdentifier().getTitle() );
+ }
+ }
+ catch( NoSuchSequenceException nsse ){
+ // we can safely ignore this
+ }
+
+ selectionRegion.setText
+ ( "[ " + rect.getX() + " - " + (rect.getX() + rect.getWidth() - 1) + " ]" );
+ }
+ else{
+ // there is no selection so clear everything
+ motifName.setText( "" );
+ sequencesListModel.clear();
+ selectionRegion.setText( "" );
+ }
+ }
+
+ public void valueChanged( AlignmentSelectionEvent event )
+ {
+ String title = model.getCurrentSelectionName();
+
+ // first do we have this one in the list
+ if( !selectionListModel.contains( title ) ){
+ selectionListModel.addElement( title );
+ // if we are sorting the motifs, the er.. sort them
+ if( sortMotifs.isSelected() ){
+ sortMotifs();
+ }
+ }
+
+ ensureOneSelection();
+
+ // in case the selected model has changed
+ updateGuiForSelection();
+ }
+
+ private MotifFormatFileChooser dirChooser;
+ private MotifFormatFileChooser fileChooser;
+
+ public void actionPerformed( ActionEvent event )
+ {
+ Object src = event.getSource();
+
+ if( src == quit ){
+ setVisible( false );
+ }
+ else if( src == motifName ){
+ if( isCurrentlySelected() ){
+ // check that the name of the current selection has changed..
+ String currentName = getCurrentlySelectedName();
+ String textName = motifName.getText();
+
+ if( currentName.equals( textName ) ) return;
+
+ setNameForSelection( currentName, textName );
+ }
+ }
+ else if( src == clearSelected ){
+ if( isCurrentlySelected() ){
+ // we want to stop listening as we know that this change is
+ // about to occur
+ model.removeAlignmentSelectionListener( this );
+ model.clearSelection( getCurrentlySelectedName() );
+ model.addAlignmentSelectionListener( this );
+ selectionListModel.remove( getCurrentlySelectedIndex() );
+ updateGuiForSelection();
+ }
+ }
+ else if( src == clearAll ){
+ clearAllSelections();
+ }
+
+ else if( src == save ){
+ if( dirChooser == null ){
+ dirChooser = new MotifFormatFileChooser();
+ dirChooser.setFileSelectionMode( JFileChooser.DIRECTORIES_ONLY );
+ dirChooser.setSelectedFile
+ ( new File( System.getProperty( "user.dir" ) ) );
+ dirChooser.setDialogTitle( "Choose Directory for save" );
+ }
+ int option = dirChooser.showSaveDialog( this );
+ if( option == JFileChooser.APPROVE_OPTION ){
+ saveMotif( dirChooser.getSelectedFile(), dirChooser.getFormat() );
+ }
+ }
+
+ else if( src == saveSelected ){
+ if( fileChooser == null ){
+ fileChooser = new MotifFormatFileChooser();
+ fileChooser.setFileSelectionMode( JFileChooser.FILES_ONLY );
+ fileChooser.setDialogTitle( "Choose File to save motif" );
+ }
+
+ if( getCurrentlySelectedName() != null ){
+ fileChooser.setSelectedFile( new File( getCurrentlySelectedName() +
+ "." + fileChooser.getFormat().toLowerCase() ) );
+ }
+
+ int option = fileChooser.showSaveDialog( this );
+ if( option == JFileChooser.APPROVE_OPTION ){
+ saveMotif( fileChooser.getSelectedFile(), getCurrentlySelectedName(), fileChooser.getFormat() );
+ }
+ }
+ else if( src == sortMotifs ){
+ setSortMotif( sortMotifs.isSelected() );
+ }
+
+ // directional increase/decrease
+ else if( src == plusNorth ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.NORTH, 1 );
+ }
+ }
+ else if( src == plusEast ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.EAST, 1 );
+ }
+ }
+ else if( src == plusSouth ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.SOUTH, 1 );
+ }
+ }
+ else if( src == plusWest ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.WEST, 1 );
+ }
+ }
+
+ else if( src == minusNorth ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.NORTH, -1 );
+ }
+ }
+ else if( src == minusEast ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.EAST, -1 );
+ }
+ }
+ else if( src == minusSouth ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.SOUTH, -1 );
+ }
+ }
+ else if( src == minusWest ){
+ if( isCurrentlySelected() ){
+ model.resizeSelection( getCurrentlySelectedName(), Direction.WEST, -1 );
+ }
+ }
+ }
+
+ private void clearAllSelections()
+ {
+ model.removeAlignmentSelectionListener( this );
+ model.clearAllSelections();
+ model.addAlignmentSelectionListener( this );
+ selectionListModel.removeAllElements();
+ updateGuiForSelection();
+ }
+
+ private void setNameForSelection( String oldname, String newname )
+ {
+ setNameAt( oldname, newname, getCurrentlySelectedIndex() );
+ }
+
+ private void setNameAt( String oldname, String newname, int at )
+ {
+ boolean cont;
+ int i = 0;
+ String tmpName = newname;
+
+ do{
+ try{
+ cont = false;
+ // set the new name
+ model.setNameForSelection( oldname, tmpName );
+
+ // update the gui
+ motifName.setText( tmpName );
+ selectionListModel.setElementAt( tmpName, at );
+ }
+ catch( IllegalArgumentException iae ){
+ // the name is not unique to we want to add an integer to the
+ // name
+ cont = true;
+ tmpName = newname + ":" + ++i;
+ }
+ }
+ while( cont );
+ }
+
+ // this class has some accessory buttons on for choosing the file
+ // format to write as. This class needs to be tied up so that it
+ // will use multiple file formats. Actually in reality this
+ // functionality needs to be moved across to the SequenceOutput
+ // module.
+ class MotifFormatFileChooser extends JFileChooser implements ActionListener
+ {
+ private String format = "MOT";
+
+ private JRadioButton mot, pir;
+
+ public MotifFormatFileChooser()
+ {
+ super();
+
+ JPanel panel = new JPanel();
+ panel.setBorder
+ ( new TitledBorder( LineBorder.createGrayLineBorder(), "Format" ) );
+ ButtonGroup group = new ButtonGroup();
+
+ mot = new JRadioButton( "Motif" );
+ group.add( mot );
+ panel.add( mot );
+ mot.addActionListener( this );
+ mot.setSelected( true );
+
+ pir = new JRadioButton( "PIR" );
+ group.add( pir );
+ panel.add( pir );
+ pir.addActionListener( this );
+
+ setAccessory( panel );
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ if( event.getSource() == mot ){
+ format = "MOT";
+ updateFormat();
+ }
+
+ if( event.getSource() == pir ){
+ format = "PIR";
+ updateFormat();
+ }
+ }
+
+ private void updateFormat()
+ {
+ File selected = getSelectedFile();
+ if( selected != null ){
+ String name = selected.getAbsolutePath();
+ String newName = name.substring( 0, name.length() - 3 ) + format.toLowerCase();
+ setSelectedFile( new File( newName ) );
+ }
+ }
+
+ public String getFormat()
+ {
+ return format;
+ }
+ }
+} // CinemaMotifFrame
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaMotifFrame.java,v $
+ * Revision 1.12 2001/07/10 14:15:24 lord
+ * Fixed a few naming bugs.
+ *
+ * Revision 1.11 2001/07/06 11:49:16 lord
+ * Changed initially selected directory for save motifs
+ *
+ * Revision 1.10 2001/06/01 15:24:11 lord
+ * Some minor cosmetic changes.
+ * Now ensure that at least one motif is selected all the time.
+ *
+ * Revision 1.9 2001/05/29 13:12:31 lord
+ * Removed ParserFactory import
+ *
+ * Revision 1.8 2001/05/29 13:06:07 lord
+ * Removed ParserFactory. Name change for Input module
+ *
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/01/31 17:44:31 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.5 2001/01/26 17:07:38 lord
+ * Removed debuging try/catch
+ *
+ * Revision 1.4 2001/01/24 20:13:48 lord
+ * Saving individual motifs implemented
+ *
+ * Revision 1.3 2001/01/23 18:00:55 lord
+ * Added sorting and saving
+ *
+ * Revision 1.2 2001/01/19 19:56:22 lord
+ * Updated due to changes in NamedAlignmentSelectionModel
+ *
+ * Revision 1.1 2001/01/19 15:52:08 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.java
new file mode 100644
index 0000000..f4b7f17
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifIdentifier.java
@@ -0,0 +1,68 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.motif; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * CinemaMotifIdentifier.java
+ *
+ *
+ * Created: Mon Jan 15 15:16:05 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaMotifIdentifier.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaMotifIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaMotifIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaMotifIdentifier CINEMA_MOTIF =
+ new CinemaMotifIdentifier
+ ( "uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifModule",
+ "Provides Cinema with the ability to interact with multiple motifs" );
+} // CinemaMotifIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaMotifIdentifier.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/19 15:52:08 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.java b/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.java
new file mode 100644
index 0000000..ab5c47d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/motif/CinemaMotifModule.java
@@ -0,0 +1,113 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.motif; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier;
+
+
+/**
+ * CinemaMotifModule.java
+ *
+ * This module is designed to handle motif selection and viewing
+ * within Cinema.
+ *
+ * Created: Wed Dec 27 14:57:33 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaMotifModule.java,v 1.5 2001/05/29 13:06:07 lord Exp $
+ */
+
+public class CinemaMotifModule extends CinemaModule implements CinemaActionProvider
+{
+ private CinemaMotifFrame motifDialog;
+ private NamedAlignmentSelectionModel model;
+
+ public void start()
+ {
+ setAlignmentSelectionModel
+ ( model = new NamedAlignmentSelectionModel() );
+ }
+
+ public Action[] getActions()
+ {
+ Action[] retn = new Action[ 1 ];
+
+ retn[ 0 ] = new AbstractAction
+ ( "Motif Manager" ){
+ public void actionPerformed( ActionEvent event )
+ {
+ if( motifDialog == null ){
+ motifDialog = new CinemaMotifFrame( model, CinemaMotifModule.this );
+ }
+ motifDialog.setVisible( true );
+ }
+ };
+
+ return retn;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaMotifModule.java,v 1.5 2001/05/29 13:06:07 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( SequenceOutputModuleIdentifier.FILE_OUTPUT );
+ return list;
+ }
+} // CinemaMotifModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaMotifModule.java,v $
+ * Revision 1.5 2001/05/29 13:06:07 lord
+ * Removed ParserFactory. Name change for Input module
+ *
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/01/31 17:44:42 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.2 2001/01/23 18:01:24 lord
+ * Requires file output module
+ *
+ * Revision 1.1 2001/01/19 15:52:08 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.java b/src/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.java
new file mode 100644
index 0000000..4decc5a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/motif/NamedAlignmentSelectionModel.java
@@ -0,0 +1,426 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.motif; // Package name inserted by JPack
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.NoSuchElementException;
+import uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel;
+import uk.ac.man.bioinf.gui.viewer.NullAlignmentSelectionModel;
+import uk.ac.man.bioinf.gui.viewer.SingleAlignmentSelectionModel;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.util.Direction;
+import java.util.Comparator;
+import java.util.Collections;
+
+
+/**
+ * NamedAlignmentSelectionModel.java
+ *
+ * Stores multiple selections each one with a name.
+ *
+ * Created: Wed Dec 27 15:20:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NamedAlignmentSelectionModel.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class NamedAlignmentSelectionModel
+ implements AlignmentSelectionModel, AlignmentSelectionListener
+{
+ // together these form a Map, of names to list
+ private List selectionInfo = new ArrayList();
+
+ private boolean isSelecting = false;
+ private AlignmentSelectionListenerSupport listenerList = new AlignmentSelectionListenerSupport();
+
+ private Comparator selectionComparator;
+
+ public void sortMotifs()
+ {
+ // we need a comparator for this sort
+ if( selectionComparator == null ){
+ selectionComparator = new Comparator(){
+ public int compare( Object obj1, Object obj2 )
+ {
+ SelectionInfo info1 = (SelectionInfo)obj1;
+ SelectionInfo info2 = (SelectionInfo)obj2;
+
+ SequenceAlignmentRectangle rect1 = info1.rect;
+ SequenceAlignmentRectangle rect2 = info2.rect;
+ return rect1.compareTo( rect2 );
+ }
+ };
+ }
+
+ // now do the sort
+ Collections.sort(selectionInfo, selectionComparator );
+
+ // and rename all selections
+ currentSelectionNumber = 1;
+ for( int i = 0; i < selectionInfo.size(); i++ ){
+ ((SelectionInfo)selectionInfo.get( i )).name
+ = "" + currentSelectionNumber++;
+ }
+ }
+
+
+ public Iterator getSelectionNameIterator()
+ {
+ return new Iterator(){
+ private Iterator iter = selectionInfo.iterator();
+ public boolean hasNext()
+ {
+ return iter.hasNext();
+ }
+
+ public Object next()
+ {
+ return ((SelectionInfo)iter.next()).name;
+ }
+
+ public void remove()
+ {
+ iter.remove();
+ }
+ };
+ }
+
+ public String getCurrentSelectionName()
+ {
+ return ((SelectionInfo)selectionInfo.get( selectionInfo.size() - 1 )).name;
+ }
+
+ private int getSelectionNameIndex( String name )
+ {
+ for( int i = 0; i < selectionInfo.size(); i++ )
+ if ( name.equals( ((SelectionInfo)selectionInfo.get( i )).name ) ){
+ return i;
+ }
+ return -1;
+ }
+
+
+ public SequenceAlignmentRectangle getSelectionForName( String name )
+ {
+ int index = getSelectionNameIndex( name );
+
+ if( index == -1 ) return null;
+
+ return ((SelectionInfo)selectionInfo.get( index ) ).rect;
+ }
+
+ public void setNameForSelection( String oldName, String newName )
+ {
+ int index = getSelectionNameIndex( oldName );
+
+ if( index == -1 ) throw new NoSuchElementException( "There is no such selection " );
+
+ if( getSelectionNameIndex( newName ) != -1 )
+ throw new IllegalArgumentException( "Names of selection must be unique" );
+
+ ((SelectionInfo)selectionInfo.get( index )).name = newName;
+ }
+
+ public void clearAllSelections()
+ {
+ while( selectionInfo.size() != 0 ){
+ clearSelection( (SelectionInfo)selectionInfo.get( 0 ) );
+ }
+ }
+
+ public void clearSelection( String name )
+ {
+ int index = getSelectionNameIndex( name );
+ clearSelection( index );
+ }
+
+
+ private void clearSelection( SelectionInfo info )
+ {
+ // find and remove the selection
+ clearSelection( selectionInfo.indexOf( info ), info );
+ }
+
+ private void clearSelection( int index )
+ {
+ clearSelection( index, (SelectionInfo)selectionInfo.get( index ) );
+ }
+
+
+ private void clearSelection( int index, SelectionInfo info )
+ {
+ if( index == -1 ) throw new NoSuchElementException( "There is no such selection " );
+
+ selectionInfo.remove( index );
+
+ // signal the event
+ listenerList.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent
+ ( this, info.rect, false ) );
+ }
+
+ // extend or shrink the selections programmatically
+ public void resizeSelection( String selection, Direction dir, int size )
+ {
+ int index = getSelectionNameIndex( selection );
+
+ if( index == -1 ) throw new NoSuchElementException( "There is no such selection " );
+
+ // if we are increasing the selection programmatically the
+ // selection itself must be over. So the first thing that we want
+ // to do make sure that the start is at top left, and stop is at
+ // bottom right, as we don't care where the start and stop are any
+ // more.
+
+ SelectionInfo info = (SelectionInfo)selectionInfo.get( index );
+
+ SequenceAlignmentRectangle rect = info.rect;
+ SequenceAlignmentPoint start = info.start;
+ SequenceAlignmentPoint stop = info.stop;
+
+ start.setLocation( rect.getLocation() );
+ stop.setLocation( rect.getLocation().getX() + rect.getWidth() - 1,
+ rect.getLocation().getY() + rect.getHeight() - 1);
+
+ // now we can move the start or stop appropriately.
+ if( dir == Direction.NORTH ){
+ start.setLocation( start.getX(), start.getY() - size );
+ }
+ else if( dir == Direction.EAST ){
+ stop.setLocation( stop.getX() + size, stop.getY() );
+ }
+ else if( dir == Direction.SOUTH ){
+ stop.setLocation( stop.getX(), stop.getY() + size );
+ }
+ else if( dir == Direction.WEST ){
+ start.setLocation( start.getX() - size, start.getY() );
+ }
+
+ recalcSelectionRectangle( rect, start, stop );
+
+ // and signal an event
+ listenerList.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent( this, rect, false ) );
+ }
+
+
+ // implementation of AlignmentSelectionModel
+ public boolean isSelecting()
+ {
+ return isSelecting;
+ }
+
+ public SequenceAlignmentRectangle getCurrentSelection()
+ {
+ return ((SelectionInfo)selectionInfo.get( selectionInfo.size() - 1 )).rect;
+ }
+
+ public int getNumberSelections()
+ {
+ return selectionInfo.size();
+ }
+
+ public SequenceAlignmentRectangle getSelectionAt( int index )
+ throws IndexOutOfBoundsException
+ {
+ return ((SelectionInfo)selectionInfo.get( index )).rect;
+ }
+
+ public boolean isPointSelected( SequenceAlignmentPoint point )
+ {
+ for( int i = 0; i < selectionInfo.size(); i++ ){
+ if( ((SelectionInfo)selectionInfo.get( i )).rect.contains( point ) ){
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public void clearSelection()
+ {
+ // we want to ignore this.
+ }
+
+ private List rectAtPointList;
+ public SequenceAlignmentRectangle[] getRectanglesAtPoint( SequenceAlignmentPoint point )
+ {
+ // have a cache list here, to save on object creation.
+ if( rectAtPointList == null ){
+ rectAtPointList = new ArrayList();
+ }
+
+ // ask all of the SingleSelectionModels for their rectangles.
+ for( int i = 0; i < selectionInfo.size(); i++ ){
+ SequenceAlignmentRectangle rect = ((SelectionInfo)selectionInfo.get( i )).rect;
+ if( rect.contains( point ) ){
+ rectAtPointList.add( rect );
+ }
+ }
+
+ // create a new array to store the results, and populate it
+ SequenceAlignmentRectangle[] retn = new SequenceAlignmentRectangle
+ [ rectAtPointList.size() ];
+ rectAtPointList.toArray( retn );
+
+ // and clear the cache list to allow GC
+ rectAtPointList.clear();
+
+ return retn;
+ }
+
+ public SequenceAlignmentRectangle getRectangleAtPoint( SequenceAlignmentPoint point )
+ {
+ // ask all of the SingleSelectionModels for their rectangles.
+ for( int i = 0; i < selectionInfo.size(); i++ ){
+ SequenceAlignmentRectangle rect = ((SelectionInfo)selectionInfo.get( i )).rect;
+ if( rect.contains( point ) ){
+ return rect;
+ }
+ }
+ return null;
+ }
+
+
+ // biologists start at 1
+ private int currentSelectionNumber = 1;
+
+ private SequenceAlignmentRectangle currentRect;
+ private SequenceAlignmentPoint currentStart;
+ private SequenceAlignmentPoint currentStop;
+
+ private void recalcSelectionRectangle()
+ {
+ recalcSelectionRectangle( currentRect, currentStart, currentStop );
+ }
+
+ private void recalcSelectionRectangle
+ ( SequenceAlignmentRectangle rect,
+ SequenceAlignmentPoint start, SequenceAlignmentPoint stop )
+ {
+ rect.setLocation( start );
+ rect.setSize( 1, 1 );
+ rect.add( stop );
+ }
+
+ public void extendSelection( SequenceAlignmentPoint point )
+ {
+ // if we have no current selection, or the current selection is
+ // not selecting anymore, then start a new one...
+ if( !isSelecting ){
+ // we are now selecting
+ isSelecting = true;
+
+ // need new start stop and point
+ currentRect = new SequenceAlignmentRectangle();
+ currentStart = new SequenceAlignmentPoint( point );
+ currentStop = new SequenceAlignmentPoint();
+
+ // add all of these to the storage structures along with a
+ // name.
+ SelectionInfo info = new SelectionInfo();
+ selectionInfo.add( info );
+
+ info.name = "" + currentSelectionNumber++;
+ info.rect = currentRect;
+ info.start= currentStart;
+ info.stop = currentStop;
+ }
+
+ // store the point that we have extend to
+ currentStop = point;
+
+ // recalc the rectangle
+ recalcSelectionRectangle();
+
+ // and signal an event
+ listenerList.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent( this, currentRect, isSelecting ) );
+ }
+
+ public void stopSelection( SequenceAlignmentPoint point )
+ {
+ // set this to false so that we start with a new selection next time.
+ isSelecting = false;
+
+ // store the final point
+ currentStop = point;
+ recalcSelectionRectangle();
+
+ listenerList.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent( this, currentRect, isSelecting ) );
+ }
+
+ public void addAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ listenerList.addAlignmentSelectionListener( listener );
+ }
+
+ public void removeAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ listenerList.removeAlignmentSelectionListener( listener );
+ }
+
+ // implementation of selection listener interface
+ public void valueChanged( AlignmentSelectionEvent event )
+ {
+ listenerList.fireAlignmentSelectionEvent( event );
+ }
+
+ // struct in which to store the data
+ class SelectionInfo
+ {
+ SequenceAlignmentPoint start;
+ SequenceAlignmentPoint stop;
+ SequenceAlignmentRectangle rect;
+ String name;
+ }
+} // NamedAlignmentSelectionModel
+
+
+
+/*
+ * ChangeLog
+ * $Log: NamedAlignmentSelectionModel.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/01/23 18:02:37 lord
+ * Changed internal implementation again. Now has a single list, with an
+ * struct to hold the various information. The point is that this makes
+ * it a lot easier to sort.
+ *
+ * Revision 1.2 2001/01/19 19:57:19 lord
+ * Totally re-worked. This no longer uses the SingleAlignmentSelection model
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.java b/src/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.java
new file mode 100644
index 0000000..81a1d42
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/CinemaResources.java
@@ -0,0 +1,211 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.resources; // Package name inserted by JPack
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.io.FileNotFoundException;
+
+
+/**
+ * CinemaResources.java
+ *
+ * The purpose of this class is to provide access to the resources
+ * that cinema needs in a manner which is appropriate and simple both
+ * during development time and after deployment.
+ *
+ *
+ * Created: Mon May 29 16:44:01 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaResources.java,v 1.9 2001/05/04 12:30:33 lord Exp $
+ */
+
+public class CinemaResources
+{
+
+ public static URL getResource( String name )
+ {
+ try{
+ if( fetchCinemaDirectoryString() != null ){
+ return new File( fetchCinemaDirectoryString() + name ).toURL();
+ }
+ else{
+ return CinemaResources.class.getResource( name );
+ }
+ }
+ catch( MalformedURLException mfu ){
+ }
+ return null;
+ }
+
+ /*
+ * Defines the way in which XML load names are translated into
+ * actual XML files. The way this works at the moment is as
+ * follows.
+ *
+ * First the user config directory is searched for a file with the
+ * name of the parameter. This gives the user the ability to
+ * override any of the config provided for by Cinema. The user
+ * config directory probably needs to be configurable, but for the
+ * moment I have hard coded it as ~/.cinema/config. To ensure that
+ * this overriding does not occur by chance, all the config files
+ * specified by Cinema itself will be named with the cinema-*
+ * prefix.
+ *
+ * After this the
+ * cinema application config is searched. This happens in one of two
+ * ways, which enable Cinema to access configuration either as a jar
+ * file or during development. If the command line parameter
+ * -Dcinema.dir is specified, then this is used as the
+ * root. Alternatively if there is not specified an attempt is made
+ * to retrieve the XML file as Class resource.
+ */
+ private static File userConfig = new File( System.getProperty( "user.home" ) +
+ System.getProperty( "file.separator" ) +
+ ".cinema" +
+ System.getProperty( "file.separator" ) +
+ "config" );
+
+ private static File userExtensions = new File( System.getProperty( "user.home" ) +
+ System.getProperty( "file.separator" ) +
+ ".cinema" +
+ System.getProperty( "file.separator" ) +
+ "ext" );
+
+ private static File userPersist = new File( System.getProperty( "user.home" ) +
+ System.getProperty( "file.separator" ) +
+ ".cinema" +
+ System.getProperty( "file.separator" ) +
+ "persist" +
+ System.getProperty( "file.separator" ) +
+ "persist.ser" );
+
+ public static File getUserExtensions()
+ {
+ return userExtensions;
+ }
+
+ public static File getUserPersist()
+ {
+ userPersist.getParentFile().mkdirs();
+ return userPersist;
+ }
+
+ public static InputStream resolveXMLLoadName( String loadName ) throws IOException
+ {
+ File loadFile = new File( userConfig, loadName );
+
+ if( loadFile.exists() ){
+ return new FileInputStream( loadFile );
+ }
+
+ if( fetchCinemaDirectoryString() != null ){
+ return new FileInputStream( fetchCinemaDirectoryString() + loadName );
+ }
+
+ InputStream stream = CinemaResources.class.getResourceAsStream( loadName );
+
+ if( stream == null ) throw new FileNotFoundException( "No load file found by the name " + loadName );
+
+ return stream;
+ }
+
+ public static InputStream getModuleDTDAsResource()
+ {
+ return CinemaResources.class.getResourceAsStream( "module.dtd" );
+ }
+
+ public static String fetchModuleSystemIdentifier()
+ {
+ try{
+ return new URL( "file", null, fetchCinemaDirectoryString() + "module.dtd" ).toString();
+ }
+ catch( MalformedURLException mue ){
+ mue.printStackTrace();
+ }
+ return null;
+ }
+
+ public static String fetchCinemaDirectoryString()
+ {
+ if( System.getProperty( "cinema.dir" ) == null ){
+ return null;
+ }
+ else{
+ return System.getProperty( "cinema.dir" );
+ }
+ }
+} // CinemaResources
+
+/*
+ * ChangeLog
+ * $Log: CinemaResources.java,v $
+ * Revision 1.9 2001/05/04 12:30:33 lord
+ * Cosmetic changes
+ *
+ * Revision 1.8 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2001/02/15 18:11:21 lord
+ * Added user extensions directory
+ *
+ * Revision 1.6 2001/01/31 17:45:40 lord
+ * Added user persist file.
+ *
+ * Revision 1.5 2001/01/26 17:06:32 lord
+ * Changed XML name resolution so that I can load from the .cinema directory
+ *
+ * Revision 1.4 2000/12/18 12:10:30 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.3 2000/12/13 16:30:42 lord
+ * Added URL resource method
+ *
+ * Revision 1.2 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ * Revision 1.1 2000/08/03 16:39:54 lord
+ * CinemaResources has been moved here from the .cinema package
+ * because this way it can access resources directly through the
+ * class getResource methods
+ *
+ * Revision 1.2 2000/06/27 13:38:01 lord
+ * Cosmetic changes
+ *
+ * Revision 1.1 2000/05/30 16:05:54 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/MakeCinemaJar b/src/uk/ac/man/bioinf/apps/cinema/resources/MakeCinemaJar
new file mode 100644
index 0000000..a0b90ef
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/MakeCinemaJar
@@ -0,0 +1,5 @@
+#!/bin/sh
+# This makes the Cinema Jar file
+
+
+/opt/java/blackdown/jdk1.2.2rc4/bin/jar cmvf uk/ac/man/bioinf/apps/cinema/resources/manifest.mf cinema.jar uk/*
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/build-install.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/build-install.xml
new file mode 100644
index 0000000..d84e8f0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/build-install.xml
@@ -0,0 +1,133 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE project PUBLIC "-//ANT//DTD project//EN" "project.dtd">
+
+<!-- This build file is for building and installing current versions -->
+<!-- of Cinema. -->
+<project name="cinema" default="build-cinema" basedir=".">
+
+ <property name="cinema-load-file" value="${user.home}/.ant/cinema.props" />
+ <property file="${cinema-load-file}" />
+ <!-- This is the tag name of the latest cinema release -->
+ <property name="cinema.latest.release.tag" value="release-3_0_8" />
+
+ <!-- This is the location of source files if cinema-latest is being
+ installed -->
+ <property name="latest.source" value="/home/prints/lord/src/java" />
+ <property name="temp.dir" value="/tmp" />
+ <property name="src" value="${temp.dir}" />
+ <property name="prefix" value="/usr/local" />
+ <property name="ext" value="${prefix}/lib/cinema/ext"/>
+
+ <target name="build-cinema"
+ description="Builds the latest cinema from the CVS tree" >
+ <!-- check out everything -->
+ <cvs cvsRoot=":pserver:anon at proline.sbc.man.ac.uk:/nfs/cvs"
+ package="bioinf"
+ dest="${temp.dir}"
+ command="checkout" />
+ <!-- build everything -->
+ <antcall target="build" />
+ </target>
+
+ <target name="install-cinema"
+ depends="build-cinema"
+ description="Install Cinema from the CVS tree" >
+ <!-- install -->
+ <copy file="cinema.jar" toFile="${prefix}/lib/cinema/cinema.jar" />
+ </target>
+
+ <target name="build-cinema-latest"
+ description="Build Cinema from the current source
+ version as cinema-latest">
+ <copy todir="${temp.dir}">
+ <fileset dir="${latest.source}">
+ <include name="uk/**" />
+ </fileset>
+ </copy>
+ <!-- build everything -->
+ <antcall target="build" />
+ </target>
+
+ <target name="install-cinema-latest"
+ depends="build-cinema-latest"
+ description="Install Cinema from the CVS tree" >
+ <!-- install -->
+ <copy file="cinema.jar" toFile="${prefix}/lib/cinema/cinema.jar" />
+ </target>
+
+ <target name="build-cinema-release"
+ description="Build Cinema as a given release">
+ <!-- check out everything -->
+ <cvs cvsRoot=":pserver:anon at proline.sbc.man.ac.uk:/nfs/cvs"
+ package="bioinf"
+ dest="${temp.dir}"
+ tag="${cinema.latest.release.tag}"
+ command="checkout" />
+ <antcall target="build" />
+ </target>
+
+ <target name="install-cinema-release"
+ depends="build-cinema-release"
+ description="Install Cinema as a given release">
+ <copy file="cinema.jar"
+ toFile="${prefix}/lib/cinema/cinema-${cinema.latest.release.tag}.jar"
+ />
+ </target>
+
+ <target name="clean"
+ description="Cleans files" >
+ <delete file="${temp.dir}/cinema.jar" />
+ <delete dir="${temp.dir}/uk" />
+ </target>
+
+ <target name="build"
+ description="Runs the build" >
+
+ <copy file="project.dtd"
+ toFile="${temp.dir}/uk/ac/man/bioinf/project.dtd" />
+ <copy file="project-ext.dtd"
+ toFile="${temp.dir}/uk/ac/man/bioinf/project-ext.dtd" />
+ <ant antfile="${temp.dir}/uk/ac/man/bioinf/build.xml"
+ dir="${temp.dir}/uk/ac/man/bioinf"
+ target="build" />
+ <ant antfile="${temp.dir}/uk/ac/man/bioinf/build.xml"
+ dir="${temp.dir}/uk/ac/man/bioinf"
+ target="jar" />
+ </target>
+</project>
+
+
+
+
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-calculate.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-calculate.xml
new file mode 100644
index 0000000..8b50c7a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-calculate.xml
@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+
+<!-- There are modules that do lots of calculations to produce their -->
+<!-- results. -->
+
+<configuration>
+
+ <module>
+ <name>CINEMA_MULTIPLE_CONSENSUS</name>
+ <config>
+ <tree>
+ <node>
+ <value>Options</value>
+ <node>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ </node>
+ <node>
+ <name>CINEMA_RESIZE_ELEMENTS</name>
+ </node>
+ </node>
+ </tree>
+ </config>
+ </module>
+
+
+ <!-- Configure the consensus calculation module -->
+ <module>
+ <name>CINEMA_CONSENSUS</name>
+ <config>
+ <properties>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData</paramname>
+ <value>default</value>
+ </param>
+ </properties>
+ </config>
+ </module>
+
+ <!-- Now load the consensus display module -->
+ <load>
+ <name>CINEMA_CONSENSUS_DISPLAY</name>
+ </load>
+ <start>
+ <name>CINEMA_CONSENSUS_DISPLAY</name>
+ </start>
+</configuration>
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-identifiers.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-identifiers.xml
new file mode 100644
index 0000000..4db2dec
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-identifiers.xml
@@ -0,0 +1,81 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+<!-- In this file we load as many of the identifiers as we are likely -->
+<!-- to need. The identifiers don't take up very much memory, so it -->
+<!-- does not really matter whether we load identifiers that we don't -->
+<!-- actually use. -->
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+
+<configuration>
+ <!-- Define Identifiers that we are going to use -->
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.group.CinemaGroupIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParserIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifIdentifier</class>
+ </enumeration>
+ </identifier>
+</configuration>
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-io.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-io.xml
new file mode 100644
index 0000000..00e0381
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-io.xml
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+<configuration>
+
+ <!-- Configure the input and output system -->
+
+ <!-- Configure the Sequence Input module to use the File input -->
+ <module>
+ <name>SEQ_INPUT</name>
+ <provide>
+ <name>FILE_INPUT</name>
+ </provide>
+ </module>
+
+ <!-- Configure the Sequence Output module to use the File output -->
+ <module>
+ <name>SEQ_OUTPUT</name>
+ <provide>
+ <name>FILE_OUTPUT</name>
+ </provide>
+ </module>
+
+ <module>
+ <name>FILE_INPUT</name>
+ <config>
+ <properties>
+ <param>
+ <paramname>default</paramname>
+ <value>PIR</value>
+ </param>
+ <param>
+ <paramname>PIR</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser</value>
+ </param>
+ </properties>
+ </config>
+ </module>
+
+ <module>
+ <name>FILE_OUTPUT</name>
+ <config>
+ <properties>
+ <param>
+ <paramname>default</paramname>
+ <value>PIR</value>
+ </param>
+ <param>
+ <paramname>PIR</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser</value>
+ </param>
+ <param>
+ <paramname>MOT</paramname>
+ <value>uk.ac.man.bioinf.io.parsers.MotProteinParser</value>
+ </param>
+ </properties>
+ </config>
+ </module>
+
+ <load>
+ <name>SEQ_INPUT</name>
+ </load>
+
+ <load>
+ <name>SEQ_OUTPUT</name>
+ </load>
+</configuration>
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-main.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-main.xml
new file mode 100644
index 0000000..02813b5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-main.xml
@@ -0,0 +1,96 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+<!-- This file is loaded for every main frame of Cinema that is loaded -->
+<!-- into memory. Its meant to load everything that is needed by a -->
+<!-- working Cinema -->
+
+<configuration>
+
+ <!-- Loads the identifiers -->
+ <read>cinema-identifiers.xml</read>
+
+ <!-- Load support for persistance. This needs to be done fairly
+ early!-->
+ <module>
+ <name>CINEMA_PERSIST</name>
+ <provide>
+ <name>CINEMA_FILE_PERSIST</name>
+ </provide>
+ <config>
+ </config>
+ </module>
+
+ <load>
+ <name>CINEMA_PERSIST</name>
+ </load>
+ <start>
+ <name>CINEMA_PERSIST</name>
+ </start>
+
+ <load>
+ <name>CINEMA_SYSTEM_EVENTS</name>
+ </load>
+
+ <!-- Loads the input and output modules -->
+ <read>cinema-io.xml</read>
+
+ <!-- Load the calculation modules -->
+ <read>cinema-calculate.xml</read>
+
+ <!-- Loads the viewing modules -->
+ <read>cinema-view.xml</read>
+
+ <!-- Loads the manipulation modules -->
+ <read>cinema-manipulate.xml</read>
+
+ <!-- read in the configuration for the menu system -->
+ <read>cinema-menu.xml</read>
+
+ <!-- load the user defined config -->
+ <read required='false'>main.xml</read>
+
+ <load>
+ <name>CINEMA_GO</name>
+ </load>
+ <start>
+ <name>CINEMA_GO</name>
+ </start>
+
+ <!-- the command line parser -->
+
+ <load>
+ <name>COMMAND_LINE_PARSER</name>
+ </load>
+ <start>
+ <name>COMMAND_LINE_PARSER</name>
+ </start>
+</configuration>
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-manipulate.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-manipulate.xml
new file mode 100644
index 0000000..648b86a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-manipulate.xml
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+
+<!-- Modules which manipulate the sequences or parts of them -->
+<configuration>
+ <load>
+ <name>CINEMA_GROUPS</name>
+ </load>
+
+ <load>
+ <name>CINEMA_MOTIF</name>
+ </load>
+
+ <start>
+ <name>CINEMA_GROUPS</name>
+ </start>
+
+ <load>
+ <name>CINEMA_REGEXP</name>
+ </load>
+</configuration>
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-menu.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-menu.xml
new file mode 100644
index 0000000..6d0ad90
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-menu.xml
@@ -0,0 +1,117 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+
+<!-- This file configures and loads the Cinema Menu system. I have -->
+<!-- placed this separately because its a fairly long and complex -->
+<!-- configuration, and it just complicates the main system. -->
+
+<configuration>
+
+ <!-- Configure the menu system -->
+ <module>
+ <name>CINEMA_MENU_SYSTEM</name>
+ <config>
+ <tree>
+ <!-- The File Menu -->
+ <node>
+ <value>File</value>
+ <node>
+ <!-- Provides the open alignment -->
+ <name>SEQ_INPUT</name>
+ </node>
+ <node>
+ <!-- Provides the save alignment -->
+ <name>SEQ_OUTPUT</name>
+ </node>
+ <node>
+ <!-- Provides the exit menu -->
+ <name>CINEMA_CORE_GUI</name>
+ </node>
+ </node>
+ <!-- End File Menu -->
+
+ <!-- The Edit Menu -->
+ <node>
+ <value>Edit</value>
+ <node>
+ <name>CINEMA_MOTIF</name>
+ </node>
+ <node>
+ <name>CINEMA_REGEXP</name>
+ </node>
+ </node>
+ <!-- End View Menu -->
+
+ <node>
+ <value>View</value>
+ <node>
+ <!-- Provides the ability to resize the elements of the
+ viewer -->
+ <name>CINEMA_RESIZE_ELEMENTS</name>
+ </node>
+ </node>
+
+ <!-- The Colour Menu -->
+ <node>
+ <value>Colour</value>
+ <node>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ </node>
+ </node>
+ <!-- End Colour Menu -->
+
+ <!-- The Group Menu -->
+ <node>
+ <value>Group</value>
+ <node>
+ <!-- Provides the group frame -->
+ <name>CINEMA_GROUPS</name>
+ </node>
+ </node>
+ <!-- End Group Menu -->
+
+ <!-- The Consensus Menu -->
+ <node>
+ <value>Consensus</value>
+ <node>
+ <name>CINEMA_CONSENSUS_DISPLAY</name>
+ </node>
+ </node>
+ </tree>
+ </config>
+ </module>
+
+
+ <!-- Read the menu hook to enable addition of more configuration by
+ the user -->
+ <read required='false'>menu-hook.xml</read>
+
+ <!-- Add in Menu system -->
+ <load>
+ <name>CINEMA_MENU_SYSTEM</name>
+ </load>
+ <start>
+ <name>CINEMA_MENU_SYSTEM</name>
+ </start>
+
+</configuration>
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-shared.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-shared.xml
new file mode 100644
index 0000000..158ce83
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-shared.xml
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+
+
+
+<!-- This file is loaded once per JVM for anything which is launched -->
+<!-- by Cinema. Its meant to load modules which we only need one -->
+<!-- of. Eventually it might be nice to have it load some sort of GUI -->
+<!-- module, which just has tool buttons on it, I'm not sure at the -->
+<!-- moment -->
+
+<configuration>
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <!-- Launch the debug console. Currently the Debug interface works
+ through a static calls to the Debug class, so there is really no
+ point having more than one of these anyway. -->
+
+ <!--
+ <load>
+ <name>CINEMA_DEBUG</name>
+ </load>
+ <start>
+ <name>CINEMA_DEBUG</name>
+ </start>
+ -->
+
+ <!-- Launch the splash screen -->
+ <load>
+ <name>CINEMA_SPLASH</name>
+ </load>
+ <start>
+ <name>CINEMA_SPLASH</name>
+ </start>
+
+ <!-- This module provides the Quit and Exit buttons for Cinema. Its
+ needs to be shared between all instances so that it can blank out
+ Quit when there is only one left -->
+ <load>
+ <name>CINEMA_QUIT_EXIT</name>
+ </load>
+ <start>
+ <name>CINEMA_QUIT_EXIT</name>
+ </start>
+</configuration>
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-view.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-view.xml
new file mode 100644
index 0000000..936e3a2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema-view.xml
@@ -0,0 +1,99 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+
+
+<!-- This program is free software; you can redistribute it and/or modify -->
+<!-- it under the terms of the GNU General Public License as published by -->
+<!-- the Free Software Foundation; either version 2 of the License, or -->
+<!-- (at your option) any later version. -->
+
+<!-- This program is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -->
+<!-- GNU General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU General Public License -->
+<!-- along with this program; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+<!-- This loads all of those modules which are involved with changing -->
+<!-- the way that the sequence are viewed -->
+
+<configuration>
+
+ <!-- The color selector chooses the colours that cinema displays -->
+
+ <load>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ </load>
+
+ <!-- Configuration for the colour selector module -->
+ <module>
+ <name>CINEMA_COLOR_FACTORY</name>
+ <config>
+ <properties>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.GrayScaleVariance</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.TaylorColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.ColormapColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.DefaultColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.IntenseColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.PedanticColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.VariableColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.VariationsColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.ZenecaColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ </properties>
+ </config>
+ </module>
+
+ <load>
+ <name>CINEMA_RESIZE_ELEMENTS</name>
+ </load>
+
+ <load>
+ <name>CINEMA_STATUS</name>
+ </load>
+ <start>
+ <name>CINEMA_STATUS</name>
+ </start>
+</configuration>
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema.jpg b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema.jpg
new file mode 100644
index 0000000..9de3a4f
Binary files /dev/null and b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema.jpg differ
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/cinema.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema.xml
new file mode 100644
index 0000000..b3fc553
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/cinema.xml
@@ -0,0 +1,252 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+<!-- This file is loaded for every main frame of Cinema that is loaded -->
+<!-- into memory. Its meant to load everything that is needed by a -->
+<!-- working Cinema -->
+
+<configuration>
+ <!-- Define Identifiers that we are going to use -->
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.group.CinemaGroupIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.consensus.CinemaConsensusIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.io.SequenceInputModuleInterfaceIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier>
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.io.SequenceOutputModuleInterfaceIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.io.CinemaCommandLineParserIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.motif.CinemaMotifIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <!-- Configure the Sequence Input module to use the File input -->
+ <module>
+ <name>SEQ_INPUT</name>
+ <provide>
+ <name>FILE_INPUT</name>
+ </provide>
+ <config>
+ <!-- No configuration is required at the moment -->
+ </config>
+ </module>
+
+ <!-- Configure the Sequence Output module to use the File output -->
+ <module>
+ <name>SEQ_OUTPUT</name>
+ <provide>
+ <name>FILE_SEQ_OUTPUT</name>
+ </provide>
+ <config>
+ <!-- No configuration is required at the moment -->
+ </config>
+ </module>
+
+ <!-- Load in those modules which are required by the menu system -->
+ <load>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ </load>
+
+ <load>
+ <name>CINEMA_GROUPS</name>
+ </load>
+
+ <load>
+ <name>CINEMA_RESIZE_ELEMENTS</name>
+ </load>
+
+ <load>
+ <name>SEQ_INPUT</name>
+ </load>
+
+ <load>
+ <name>SEQ_OUTPUT</name>
+ </load>
+
+ <module>
+ <name>CINEMA_MULTIPLE_CONSENSUS</name>
+ <config>
+ <tree>
+ <node>
+ <value>Options</value>
+ <node>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ </node>
+ <node>
+ <name>CINEMA_RESIZE_ELEMENTS</name>
+ </node>
+ </node>
+ </tree>
+ </config>
+ </module>
+
+ <!-- Configuration for the colour selector module -->
+ <module>
+ <name>CINEMA_COLOR_SELECTOR</name>
+ <config>
+ <properties>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.ThreadedPercentageIDVarianceColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.PercentageIDVarianceColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData</paramname>
+ <value></value>
+ </param>
+ </properties>
+ </config>
+ </module>
+
+ <!-- Configure the consensus calculation module -->
+ <module>
+ <name>CINEMA_CONSENSUS</name>
+ <config>
+ <properties>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.consensus.PercentageIDConsensusCalculatorMetaData</paramname>
+ <value></value>
+ </param>
+ <param>
+ <paramname>uk.ac.man.bioinf.apps.cinema.consensus.ThreadedPercentageIDConsensusCalculatorMetaData</paramname>
+ <value></value>
+ </param>
+ </properties>
+ </config>
+ </module>
+
+ <!-- Now load the consensus display module -->
+ <load>
+ <name>CINEMA_CONSENSUS_DISPLAY</name>
+ </load>
+ <start>
+ <name>CINEMA_CONSENSUS_DISPLAY</name>
+ </start>
+
+ <load>
+ <name>CINEMA_MOTIF</name>
+ </load>
+ <start>
+ <name>CINEMA_MOTIF</name>
+ </start>
+
+ <start>
+ <name>CINEMA_GROUPS</name>
+ </start>
+
+
+ <!-- read in the configuration for the menu system -->
+ <read>menu.xml</read>
+
+ <load>
+ <name>CINEMA_HACK</name>
+ </load>
+ <start>
+ <name>CINEMA_HACK</name>
+ </start>
+
+
+ <load>
+ <name>CINEMA_GO</name>
+ </load>
+ <start>
+ <name>CINEMA_GO</name>
+ </start>
+
+ <!-- the command line parser -->
+
+ <load>
+ <name>COMMAND_LINE_PARSER</name>
+ </load>
+ <start>
+ <name>COMMAND_LINE_PARSER</name>
+ </start>
+</configuration>
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/color-convert.el b/src/uk/ac/man/bioinf/apps/cinema/resources/color-convert.el
new file mode 100644
index 0000000..7b65844
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/color-convert.el
@@ -0,0 +1,282 @@
+;; This is just a little hack script that I wrote to generate Colour
+;; map meta data classes based on a standard scheme.
+
+
+
+;; does hex convert
+(require 'hexl)
+
+;; does the string replace
+(defun color-convert-match( one-letter )
+ (cond ((string= one-letter "A")
+ "AminoAcid.ALANINE" )
+ ((string= one-letter "R")
+ "AminoAcid.ARGININE" )
+ ((string= one-letter "N")
+ "AminoAcid.ASPARAGINE" )
+ ((string= one-letter "D")
+ "AminoAcid.ASPARTICACID" )
+ ((string= one-letter "C")
+ "AminoAcid.CYSTEINE" )
+ ((string= one-letter "Q")
+ "AminoAcid.GLUTAMINE" )
+ ((string= one-letter "E")
+ "AminoAcid.GLUTAMICACID" )
+ ((string= one-letter "G")
+ "AminoAcid.GLYCINE" )
+ ((string= one-letter "H")
+ "AminoAcid.HISTIDINE" )
+ ((string= one-letter "I")
+ "AminoAcid.ISOLEUCINE" )
+ ((string= one-letter "L")
+ "AminoAcid.LEUCINE" )
+ ((string= one-letter "K")
+ "AminoAcid.LYSINE" )
+ ((string= one-letter "M")
+ "AminoAcid.METHIONINE" )
+ ((string= one-letter "F")
+ "AminoAcid.PHENYLALANINE" )
+ ((string= one-letter "P")
+ "AminoAcid.PROLINE" )
+ ((string= one-letter "S")
+ "AminoAcid.SERINE" )
+ ((string= one-letter "T")
+ "AminoAcid.THREONINE" )
+ ((string= one-letter "W")
+ "AminoAcid.TRYPTOPHAN" )
+ ((string= one-letter "Y")
+ "AminoAcid.TYROSINE" )
+ ((string= one-letter "V")
+ "AminoAcid.VALINE" )
+ ((string= one-letter "B")
+ "AminoAcid.ASNORASP" )
+ ((string= one-letter "Z")
+ "AminoAcid.GLUORGLN" )
+ ((string= one-letter "X" )
+ "AminoAcid.ANY" )
+ (t
+ (error "Unknown letter %s" one-letter ))))
+
+
+
+(defun color-convert()
+ "Create a new buffer based on the current buffer, which has the
+Java class for doing colours"
+ (interactive)
+ (let* ((from-buffer (current-buffer))
+ (scheme-name
+ (read-from-minibuffer
+ "Colour Scheme Name: "
+ (capitalize
+ (file-name-nondirectory
+ (file-name-sans-extension
+ (buffer-file-name from-buffer))))))
+ (buffer-name "*color-convert*")
+ (exist-buffer (get-buffer buffer-name))
+ (to-buffer
+ (progn
+ (if exist-buffer
+ (kill-buffer exist-buffer))
+ (get-buffer-create buffer-name))))
+ (switch-to-buffer to-buffer)
+ ;; do the conversion
+ (color-convert-insert-preamble to-buffer scheme-name)
+ (color-convert-convert-buffer to-buffer from-buffer)
+ (color-convert-insert-postamble to-buffer)
+ ;; suppress normal mode selection. Other wise I
+ ;; get silly folding that I dont want.
+ (let((change-major-mode-with-file-name 'nil))
+ (set-visited-file-name
+ (concat scheme-name "ColorMapMetaData.java"))
+ (java-mode))
+ ;; reindent
+ (goto-char (point-min))
+ (indent-according-to-mode)
+ (while (= 0 (forward-line))
+ (indent-according-to-mode))
+ (normal-mode)
+ (goto-char (point-min))
+ ;; this is a good point to be.
+ (search-forward "class")))
+
+(defun color-convert-insert-preamble( buffer name )
+ (set-buffer buffer)
+ (insert-string
+"/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.color;
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * THIS FILE WAS AUTOMATICALLY GENERATED USING color-convert.el
+ *
+ * Created: Wed Jul 19 14:31:39 2000
+ *
+ * @author color-convert.el
+ * @version $Id: color-convert.el,v 1.1 2001/07/06 12:34:37 lord Exp $
+ */
+
+public class ")
+ (insert-string name)
+ (insert-string
+"ColorMapMetaData implements ColorMapMetaData
+{
+ // we only need one!
+ private static final IndividualElementColorMap map;
+ public static final String NAME = \"")
+ (insert-string name)
+ (insert-string " Color Scheme\";
+
+ static
+ {
+ // color mapping
+ Element[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length + 1];
+ for (int i = 0; i < aa.length; i++) {
+ if( false ){
+ }
+"))
+
+
+(defun color-convert-insert-postamble(buffer)
+ (set-buffer buffer)
+ (insert-string
+ (concat
+ "}
+ colors[ aa.length ] = new Color( "
+ color-convert-default-color " );"))
+ (insert-string "
+
+
+
+ Element[] elem = new Element[ aa.length + 1 ];
+ System.arraycopy( aa, 0, elem, 0, aa.length );
+ elem[ aa.length ] = Gap.gap;
+
+ map = new IndividualElementColorMap( NAME, elem, colors);
+
+ }
+
+ public void setModule( CinemaModule module )
+ {
+ // nothing required
+ }
+
+ public String getColorMapName()
+ {
+ return NAME;
+ }
+
+ public ColorMap getInstance( SequenceAlignment alignment, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+
+ public ColorMap getConsensusInstance( ConsensusSequence sequence, JAlignmentViewer viewer )
+ {
+ return map;
+ }
+}"))
+
+(defun color-convert-convert-buffer(to-buffer from-buffer)
+ (set-buffer from-buffer)
+ (goto-char (point-min))
+ (color-convert-convert-line to-buffer from-buffer)
+ ;;now insert the default colour
+ (set-buffer to-buffer)
+ (insert-string
+ (concat "else
+colors[ i ] = new Color( " color-convert-default-color " );
+")))
+
+
+(defvar color-convert-gap-color nil)
+(defvar color-convert-default-color nil)
+
+(defun color-convert-convert-line(to-buffer from-buffer)
+ "Convert a line at a time"
+ (let* ((point (point))
+ (amino-acid
+ (buffer-substring-no-properties
+ point
+ (+ 1 point)))
+ (colour
+ (buffer-substring-no-properties
+ (+ 2 point)
+ (+ 8 point))))
+ (cond
+ ;; check for terminiation
+ ((string= "<" amino-acid)
+ nil)
+ ((string= " " amino-acid)
+ (progn
+ (setq color-convert-default-color
+ (color-convert-hex-to-int-string colour))
+ (forward-line)
+ (color-convert-convert-line to-buffer from-buffer)))
+ ((string= "-" amino-acid)
+ (progn
+ (setq color-convert-gap-color
+ (color-convert-hex-to-int-string colour))
+ (forward-line)
+ (color-convert-convert-line to-buffer from-buffer)))
+ (t
+ (progn
+ (save-excursion
+ (set-buffer to-buffer)
+ (insert-string
+ "else if ( aa[ i ] == ")
+ (insert-string (color-convert-match amino-acid))
+ (insert-string
+ ")
+colors[ i ] = new Color( ")
+ (insert-string (color-convert-hex-to-int-string colour))
+ (insert-string " );
+"))
+ (forward-line)
+ (color-convert-convert-line to-buffer from-buffer))))))
+
+(defun color-convert-hex-to-int-string( number )
+ (mapconcat
+ 'hexl-hex-string-to-integer
+ (list
+ (substring colour 0 2)
+ (substring colour 2 4)
+ (substring colour 4 6))
+ " , "))
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/manifest.mf b/src/uk/ac/man/bioinf/apps/cinema/resources/manifest.mf
new file mode 100644
index 0000000..9648c3d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/manifest.mf
@@ -0,0 +1 @@
+Main-Class : uk.ac.man.bioinf.apps.cinema.Cinema
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/module.dtd b/src/uk/ac/man/bioinf/apps/cinema/resources/module.dtd
new file mode 100644
index 0000000..3aeae81
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/module.dtd
@@ -0,0 +1,127 @@
+<?xml encoding="UTF-8"?>
+
+
+<!ELEMENT configuration (identifier*, module*, load*, start*, read*)>
+
+<!-- defines a Java class. Used in several places -->
+<!ELEMENT class (#PCDATA) >
+
+<!-- defines a module name -->
+<!ELEMENT name (#PCDATA) >
+
+<!--
+ Identifier:- This defines an indentifier for a module. There
+ are two ways of doing this, which offer a nice comprimise
+ between type safety within Java and genericity outside of it.
+
+ These two types are
+ 1) Enumeration. This is an identifier which extends
+ uk.ac.man.bioinf.util.AbstractEnumeration. This
+ should also implement ModuleIdentifier, and all the
+ elements of this class should each identify a single
+ module. Although it is not required it is recommended
+ Enumerations of this type actually extend from
+ uk.ac.man.bioinf.module.AbstractEnumeratedIdentifier.
+ This class ensures (or will do when its written!
+ PENDING:- PL) that the module name returned by an
+ object is the same as the variable name which holds
+ a reference to that object. This should ease
+ debugging.
+
+ 2) Generic. These are identifiers specified by the class
+ uk.ac.man.bioinf.module.GenericIdentifier, where both
+ the module name, and the class name is defined within
+ the XML. Instances of this class must be obtained
+ from the GenericIdentifier.resolveIdentifier( String )
+ within Java which at least has the advantage of being
+ fail-fast if not type safe.
+-->
+<!ELEMENT identifier (enumeration|generic)>
+
+<!--
+ There are two types of modules, which are those
+ defined by classes and those defined by interfaces. For those
+ defined by interfaces there should also be a module which
+ implements this interface, and will provide the object that is
+ actually returned when the interface module is requested.
+ PENDING:- PL. It would be possible to require that a concrete
+ module be specified when the interface is defined but Ive
+ decided not to. The idea is that you might want to define
+ modules in one file and the implementation in another.
+-->
+<!ATTLIST identifier concrete (true|false) 'true'>
+
+<!ELEMENT enumeration (class)>
+<!ELEMENT generic (class,name)>
+
+
+<!--
+ This tag is for module configuration. This bit is fairly open
+ at the moment.
+-->
+<!ELEMENT module (name, provide?,config)>
+
+<!--
+ This is a module which is providing the concrete
+ implementation for an interface module.
+-->
+<!ELEMENT provide (name)>
+
+
+<!--
+ This is the configuration for this module. This bit is totally
+ open at the moment. Eventually it should several tags which
+ map to various data structures that I might want to use as
+ configuration. Also I havent worked out what to do yet for
+ interfaces modules. Should I just add the configurations
+ together or what?
+-->
+<!ELEMENT config (properties?,tree?)>
+
+<!--
+ What to do with this config.
+ replace - replace any existing configuration for this module
+ add - add to any existing configuration. Note that the properties
+ configuration will still overwrite any other property with the same name
+-->
+<!ATTLIST config mode (replace|add) 'add'>
+
+
+<!--
+ A properties list
+-->
+<!ELEMENT properties (param+)>
+<!ELEMENT param ((paramname, (value|name))+)>
+<!ELEMENT paramname (#PCDATA)>
+<!ELEMENT value (#PCDATA)>
+
+<!--
+ A tree structure
+-->
+<!ELEMENT tree (node*)>
+<!ELEMENT node ((value|name), node*)>
+
+
+<!--
+ Actually load an instance of a module at this point
+-->
+<!ELEMENT load (name)>
+
+<!--
+ Start an instance of a module at this point
+-->
+<!ELEMENT start (name)>
+
+<!--
+ Read another XML file. I think that this should leave fairly
+ open how the file is specified, and where it is looked for.
+-->
+<!ELEMENT read (#PCDATA)>
+
+<!--
+ If true and the file is not found then an error will be thrown,
+ otherwise it will be silently ignored
+-->
+<!ATTLIST read required (true|false) 'true'>
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/resources/shared.xml b/src/uk/ac/man/bioinf/apps/cinema/resources/shared.xml
new file mode 100644
index 0000000..a2b3336
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/resources/shared.xml
@@ -0,0 +1,77 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE configuration SYSTEM "module.dtd">
+
+<!-- This file is loaded once per JVM for anything which is launched -->
+<!-- by Cinema. Its meant to load modules which we only need one -->
+<!-- of. Eventually it might be nice to have it load some sort of GUI -->
+<!-- module, which just has tool buttons on it, I'm not sure at the -->
+<!-- moment -->
+
+<configuration>
+ <identifier concrete="true">
+ <enumeration>
+ <class>uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedIdentifier</class>
+ </enumeration>
+ </identifier>
+
+ <!-- Launch the debug console. Currently the Debug interface works
+ through a static calls to the Debug class, so there is really no
+ point having more than one of these anyway. -->
+ <load>
+ <name>CINEMA_DEBUG</name>
+ </load>
+ <start>
+ <name>CINEMA_DEBUG</name>
+ </start>
+
+ <!-- Launch the splash screen -->
+ <load>
+ <name>CINEMA_SPLASH</name>
+ </load>
+ <start>
+ <name>CINEMA_SPLASH</name>
+ </start>
+
+ <!-- This module provides the Quit and Exit buttons for Cinema. Its
+ needs to be shared between all instances so that it can blank out
+ Quit when there is only one left -->
+ <load>
+ <name>CINEMA_QUIT_EXIT</name>
+ </load>
+ <start>
+ <name>CINEMA_QUIT_EXIT</name>
+ </start>
+</configuration>
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.java b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.java
new file mode 100644
index 0000000..0ace7fc
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaDebug.java
@@ -0,0 +1,328 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.shared; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import javax.swing.ButtonGroup;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier;
+import uk.ac.man.bioinf.apps.invoker.Invoker;
+import uk.ac.man.bioinf.debug.AbstractDebug;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.debug.DebugInterface;
+import uk.ac.man.bioinf.debug.DebugMultiplexer;
+import uk.ac.man.bioinf.debug.DefaultDebug;
+import uk.ac.man.bioinf.debug.DefaultFileDebug;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaDebug.java
+ *
+ * This class provides the Debugging architecture implementation for
+ * Cinema. It provides a Console GUI, files logs and oh so much more...
+ *
+ * Eventually the initial state of this should result from the XML
+ * initiation, but at the moment it just does lots of things at once.
+ *
+ * Created: Sun May 7 18:36:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaDebug.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaDebug extends Module implements ActionListener
+{
+ private DebugImpl dImpl = new DebugImpl();
+ private DebugInterface standardOutInterface, fileOutInterface;
+
+ private JFrame frame;
+ private JTextArea area;
+ private JMenuItem standardOutOn, standardOutOff, dumpToStandardOut;
+ private JMenuItem fileOutOn, fileOutOff, dumpToFile;
+
+ public void load()
+ {
+ Debug.message( this, "Cinema Debug: Load" );
+
+ // do the gui. Eventually this should be done only if the config
+ // information says to....
+ frame = new JFrame( "Cinema Debug Console" );
+ // basic console
+ area = new JTextArea();
+ JScrollPane scroll = new JScrollPane( area );
+ frame.getContentPane().add( scroll );
+
+ // menu bar
+ JMenuBar mb = new JMenuBar();
+ frame.setJMenuBar( mb );
+ JMenu options = new JMenu( "Options" );
+ mb.add( options );
+
+ // standard out tracing
+ ButtonGroup standardOut = new ButtonGroup();
+ standardOutOn = new JRadioButtonMenuItem( "Trace to stout" );
+ standardOutOn.addActionListener( this );
+ standardOut.add( standardOutOn );
+ options.add( standardOutOn );
+ standardOutOff = new JRadioButtonMenuItem( "No trace to stout" );
+ standardOutOff.addActionListener( this );
+ standardOut.add( standardOutOff );
+ standardOut.setSelected( standardOutOff.getModel(), true );
+ options.add( standardOutOff );
+
+ // standard out dump
+ dumpToStandardOut = new JMenuItem( "Dump contents to stout" );
+ dumpToStandardOut.addActionListener( this );
+ options.add( dumpToStandardOut );
+ options.addSeparator();
+
+ // file dumping gui controls
+ ButtonGroup fileOut = new ButtonGroup();
+ fileOutOn = new JRadioButtonMenuItem( "Trace to file" );
+ fileOutOn.addActionListener( this );
+ fileOut.add( fileOutOn );
+ options.add( fileOutOn );
+ fileOutOff = new JRadioButtonMenuItem( "No trace to file" );
+ fileOutOff.addActionListener( this );
+ fileOut.add( fileOutOff );
+ fileOut.setSelected( fileOutOff.getModel(), true );
+ options.add( fileOutOff );
+
+ // file out dump
+ dumpToFile = new JMenuItem( "Dump contents to file" );
+ dumpToFile.addActionListener( this );
+ options.add( dumpToFile );
+ }
+
+ public void start()
+ {
+ Debug.message( this, "Cinema Debug: Start" );
+ frame.setSize( 200, 400 );
+ frame.setVisible( true );
+
+ // install into the Debug architecture
+ DebugMultiplexer.addDebugInstance
+ ( dImpl );
+ DebugMultiplexer.addDebugInstance
+ ( standardOutInterface = new DefaultDebug() );
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ if( event.getSource() == standardOutOff && standardOutInterface != null ){
+ DebugMultiplexer.removeDebugInstance( standardOutInterface );
+ standardOutInterface = null;
+ }
+
+ if( event.getSource() == standardOutOn && standardOutInterface == null ){
+ DebugMultiplexer.addDebugInstance( standardOutInterface = new DefaultDebug() );
+ }
+
+ if( event.getSource() == dumpToStandardOut ){
+ System.out.println( "\nCinema Debug Console: Dumping to standard out\n" );
+ System.out.println( area.getText() );
+ System.out.println( "Cinema Debug Console: Dump to standard out complete\n" );
+ }
+
+ if( event.getSource() == fileOutOn ){
+ File file = selectWriteFile();
+
+
+ try{
+ if( file != null ){
+ if( fileOutInterface != null ){
+ DebugMultiplexer.removeDebugInstance( fileOutInterface );
+ }
+ if( Debug.debug ){
+ Debug.message( this, "Installing debug tracing to " + file );
+ }
+ DebugMultiplexer.addDebugInstance
+ ( fileOutInterface = new DefaultFileDebug( file ) );
+ }
+ }
+ catch( IOException io ){
+ // (PENDING:- PL) Need to have something better here, once I
+ // have generic method for informing the user of problems,
+ // which should probably be through the CinemaCoreView
+ if( Debug.debug ){
+ Debug.throwable( this, io );
+ }
+ }
+ }
+
+ if( event.getSource() == fileOutOff && fileOutInterface != null ){
+ DebugMultiplexer.removeDebugInstance( fileOutInterface );
+ fileOutInterface = null;
+ }
+
+ if( event.getSource() == dumpToFile ){
+ File file = selectWriteFile();
+ try{
+ if( file != null ){
+ PrintWriter write = new PrintWriter( new FileWriter( file ) );
+ write.println( area.getText() );
+ write.close();
+ }
+ }
+ catch( IOException io ){
+ if( Debug.debug ){
+ Debug.throwable( this, io );
+ }
+ }
+ }
+ }
+
+ private File selectWriteFile()
+ {
+ JFileChooser fileChooser = new JFileChooser();
+ int option = fileChooser.showSaveDialog( frame );
+ File chosenFile = fileChooser.getSelectedFile();
+
+ if( option == fileChooser.APPROVE_OPTION && chosenFile != null ){
+ return chosenFile;
+ }
+ return null;
+ }
+
+ public String getVersion()
+ {
+ return "$version: $";
+ }
+
+ private void message( Class cla, String message )
+ {
+ //defaultDeb.message( cla, message );
+ if( SwingUtilities.isEventDispatchThread() ){
+ area.append
+ ( formMessageString( message ) );
+ }else{
+ SwingUtilities.invokeLater
+ ( new Invoker( this, formMessageString( message ) )
+ {
+ public void doRun()
+ {
+ CinemaDebug.this.area.append( (String)getParameter() );
+ }
+ });
+ }
+ }
+
+ private String formMessageString( String message )
+ {
+ return "Debug Message: " + message + "\n";
+ }
+
+ private void throwable( Class cla, Throwable th )
+ {
+ //defaultDeb.throwable( cla, th );
+ if( SwingUtilities.isEventDispatchThread() ){
+ area.append( formStackTraceString( th ) );
+ }else{
+ // (PENDING:- PL) Theres a difficulty here. This should really
+ // be done with the CinemaInvoker module, because that will have
+ // the ExceptionHandler set. The difficult here is that the
+ // ExceptionHandler will probably go through this class, and so
+ // we have the first problem with which one to load first....
+ SwingUtilities.invokeLater
+ ( new Invoker( this, formStackTraceString( th ) )
+ {
+ public void doRun()
+ {
+ CinemaDebug.this.area.append( (String)getParameter() );
+ }
+ });
+ }
+ }
+
+ private String formStackTraceString( Throwable th )
+ {
+ StringWriter str = new StringWriter();
+ th.printStackTrace( new PrintWriter( str ) );
+ return
+ "Debug Throwable: " + th +
+ "Debug Stack: " + str.toString() + "\n";
+ }
+
+ public class DebugImpl extends AbstractDebug
+ {
+ public void message( Class cla, String message )
+ {
+ CinemaDebug.this.message( cla, message );
+ }
+
+ public void throwable( Class cla, Throwable th )
+ {
+ CinemaDebug.this.throwable( cla, th );
+ }
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaUtilityIdentifier.CINEMA_INVOKER );
+ return list;
+ }
+} // CinemaDebug
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaDebug.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/15 17:31:08 lord
+ * Initial checking.
+ *
+ * Revision 1.3 2000/05/30 16:16:57 lord
+ * Import sorting, and module package completion
+ *
+ * Revision 1.2 2000/05/15 16:23:17 lord
+ * Reflecting changes in module method names
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.java
new file mode 100644
index 0000000..d2e9bd7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedIdentifier.java
@@ -0,0 +1,74 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.shared; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * CinemaSharedIdentifier.java
+ *
+ *
+ * Created: Fri Sep 15 13:45:25 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaSharedIdentifier.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaSharedIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaSharedIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final CinemaSharedIdentifier CINEMA_SPLASH =
+ new CinemaSharedIdentifier( "uk.ac.man.bioinf.apps.cinema.shared.CinemaSplash", "Splash Screen for Cinema" );
+ public static final CinemaSharedIdentifier CINEMA_DEBUG =
+ new CinemaSharedIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaDebug", "Debug Console for Cinema" );
+ public static final CinemaSharedIdentifier CINEMA_QUIT_EXIT =
+ new CinemaSharedIdentifier( "uk.ac.man.bioinf.apps.cinema.shared.CinemaSharedQuitExit",
+ "Provides the underlying support for the CinemaQuitExit men" );
+} // CinemaSharedIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaSharedIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/13 16:30:57 lord
+ * Added splash module
+ *
+ * Revision 1.1 2000/09/15 17:31:08 lord
+ * Initial checking.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.java b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.java
new file mode 100644
index 0000000..428a612
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSharedQuitExit.java
@@ -0,0 +1,150 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.shared; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreGui;
+import uk.ac.man.bioinf.module.Module;
+
+
+/**
+ * CinemaSharedQuitExit.java
+ *
+ *
+ * Created: Fri Sep 15 13:51:24 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaSharedQuitExit.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaSharedQuitExit extends Module
+{
+ private int numberOfCinemaInstances = 0;
+ private ArrayList manList = new ArrayList();
+
+ public Action[] getActions( CinemaCoreGui gui )
+ {
+ // every time this is got we need to add a new module to the
+ // number of instances.
+ numberOfCinemaInstances++;
+ QuitExitManager instance = new QuitExitManager( gui );
+ Action[] retn = instance.getActions();
+ if( manList.size() == 0 ){
+ instance.disableQuit();
+ }
+
+ if( manList.size() == 1 ){
+ ((QuitExitManager)manList.get( 0 )).enableQuit();
+ }
+
+ manList.add( instance );
+
+ return retn;
+ }
+
+ private void removeQuitExitManager( QuitExitManager man )
+ {
+ manList.remove( man );
+
+ if( manList.size() == 1 ){
+ ((QuitExitManager)manList.get( 0 )).disableQuit();
+ }
+ }
+
+ class QuitExitManager
+ {
+ private CinemaCoreGui gui;
+ private Action quit;
+
+ QuitExitManager( CinemaCoreGui gui )
+ {
+ this.gui = gui;
+ }
+
+ public void disableQuit()
+ {
+ quit.setEnabled( false );
+ }
+
+ public void enableQuit()
+ {
+ quit.setEnabled( true );
+ }
+
+ public Action[] getActions()
+ {
+ Action[] retn = new Action[ 2 ];
+ quit = retn[ 0 ] = new AbstractAction( "Close" )
+ {
+ public void actionPerformed( ActionEvent event )
+ {
+ // (PENDING:- PL) Clearly some user checking here would be a
+ // good thing.
+ QuitExitManager.this.gui.getContext().getModuleFactory().destroy();
+ removeQuitExitManager( QuitExitManager.this );
+ }
+ };
+
+ retn[ 1 ] = new AbstractAction( "Exit" )
+ {
+ public void actionPerformed( ActionEvent event )
+ {
+ QuitExitManager.this.gui.attemptSystemExit();
+ }
+ };
+ return retn;
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaSharedQuitExit.java,v 1.4 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaSharedQuitExit
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaSharedQuitExit.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/13 16:31:10 lord
+ * Removed debug
+ *
+ * Revision 1.2 2000/10/19 17:44:28 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/09/15 17:31:08 lord
+ * Initial checking.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.java b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.java
new file mode 100644
index 0000000..420aee9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/shared/CinemaSplash.java
@@ -0,0 +1,138 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.shared; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.MediaTracker;
+import java.awt.Toolkit;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import javax.swing.ImageIcon;
+import javax.swing.JEditorPane;
+import javax.swing.JLabel;
+import javax.swing.JScrollPane;
+import javax.swing.JWindow;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
+import uk.ac.man.bioinf.module.ModuleException;
+
+
+/**
+ * CinemaSplash.java
+ *
+ *
+ * Created: Tue Dec 12 17:42:27 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaSplash.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaSplash extends CinemaModule
+{
+ private JWindow splash;
+
+ public void load() throws ModuleException
+ {
+ splash = new JWindow();
+
+
+ Container contentPane = splash.getContentPane();
+
+ contentPane.setLayout(new BorderLayout());
+
+
+ //JEditorPane editorPane = new JEditorPane();
+ //editorPane.setEditable(false);
+ //editorPane.setPreferredSize(new Dimension(300, 240));
+
+ //try {
+ // editorPane.setPage
+ // ( CinemaResources.getResource( "cinema.html" ) );
+ //} catch (IOException e) {
+ // throw new ModuleException( e );
+ //}
+
+ //contentPane.add( editorPane, BorderLayout.CENTER );
+
+ JLabel label = new JLabel();
+ ImageIcon icon = new ImageIcon( CinemaResources.getResource( "cinema.jpg" ) );
+ label.setIcon( icon );
+
+ Dimension screensize = Toolkit.getDefaultToolkit().getScreenSize();
+ contentPane.add( label, BorderLayout.CENTER );
+
+ int height = icon.getIconHeight();
+ int width = icon.getIconWidth();
+
+ int x = (screensize.width - width) / 2;
+ int y = (screensize.height - height) / 2;
+
+ splash.setBounds( x, y, width, height );
+ splash.toFront();
+
+ splash.show();
+ }
+
+ public void killSplash()
+ {
+ if( splash != null ){
+ splash.setVisible( false );
+ splash.dispose();
+ splash = null;
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaSplash.java,v 1.4 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaSplash
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaSplash.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/01/15 18:49:36 lord
+ * Removed debug output
+ *
+ * Revision 1.2 2000/12/13 16:37:38 lord
+ * Removed extraneous splash
+ *
+ * Revision 1.1 2000/12/13 16:31:24 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.java
new file mode 100644
index 0000000..f5741b8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaAlignmentFrame.java
@@ -0,0 +1,329 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.util.Dictionary;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenuBar;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JViewport;
+import javax.swing.border.MatteBorder;
+import uk.ac.man.bioinf.gui.optionable.OptionableJFrame;
+import uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentRuler;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.gui.viewer.JChangedScrollPane;
+import uk.ac.man.bioinf.gui.viewer.MultiplexerFastAlignmentViewerCellRenderer;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import java.util.HashMap;
+import java.awt.Dimension;
+
+
+/**
+ * CinemaAlignmentFrame.java
+ *
+ * This class provides a basic CinemaAlignmentFrame which consists of
+ * a JScrollPane, with an JAlignmentViewer in the middle,
+ * JAlignmentButton panel down the right hand side and a
+ * JAlignmentRuler across the bottom.
+ *
+ * Created: Tue Jun 20 15:01:39 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaAlignmentFrame.java,v 1.12 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaAlignmentFrame extends OptionableJFrame implements PropertyChangeListener
+{
+ private JPanel mainPanel, rulerPanel, rowHeadersPanel;
+ private JAlignmentViewer viewer;
+ private JScrollPane scrollPane;
+ private JAlignmentButtonPanel rowHeaders;
+ private JAlignmentRuler ruler;
+ private Dimension initialCellSize;
+
+ public CinemaAlignmentFrame( String optionableName, String title, SequenceAlignment alignment )
+ {
+ this( optionableName, title );
+ setSequenceAlignment( alignment );
+ }
+
+ public CinemaAlignmentFrame( String optionableName, String title )
+ {
+ this( optionableName, title, false );
+ }
+
+ public CinemaAlignmentFrame( String optionableName, String title, boolean delayOptionable )
+ {
+ super( optionableName, title, delayOptionable );
+ setDefaultCloseOperation( JFrame.DISPOSE_ON_CLOSE );
+
+ // set up a main panel to hold the scroll pane
+ mainPanel = new JPanel();
+ mainPanel.setLayout( new BorderLayout() );
+
+ // start up the main viewer
+ viewer = new JAlignmentViewer();
+ viewer.setFastCellRenderer
+ ( new MultiplexerFastAlignmentViewerCellRenderer( viewer ) );
+ viewer.addPropertyChangeListener( this );
+
+ // need the main scroll pane.
+ scrollPane = new JChangedScrollPane
+ ( new InvertedScrollPaneLayout(),
+ viewer,
+ JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED );
+
+ // enable the performance enhancements.
+ enableScrollPanePerformance( scrollPane.getViewport() );
+
+ // this ensures that the default ruler fits the screen
+ rulerPanel = new JPanel();
+ rulerPanel.setLayout( new BorderLayout() );
+ rulerPanel.setBorder( new MatteBorder( 5, 0, 5, 0, getBackground() ) );
+
+ // install the ruler.
+ ruler = new JAlignmentRuler();
+
+ // install the column header
+ rowHeaders = new JAlignmentButtonPanel();
+
+ // this bit ensures that the rowHeader takes up only its preferred
+ // size, and it not resized bigger than that. BorderLayout always
+ // grows the CENTER component to take up excess, even when there
+ // is not CENTER component!
+ rowHeadersPanel = new JPanel();
+ rowHeadersPanel.setLayout( new BorderLayout() );
+ rowHeadersPanel.add( rowHeaders, BorderLayout.NORTH );
+ scrollPane.setRowHeaderView( rowHeadersPanel );
+ rowHeaders.setBackground( viewer.getBackground() );
+
+
+ scrollPane.setColumnHeaderView( rulerPanel );
+ rulerPanel.add( ruler, BorderLayout.WEST );
+
+ setJMenuBar( new JMenuBar() );
+
+ getContentPane().add( mainPanel );
+ mainPanel.add( scrollPane, BorderLayout.CENTER );
+
+ if( initialCellSize != null ){
+ int width = (int)initialCellSize.getWidth();
+ int height = (int)initialCellSize.getHeight();
+
+ viewer.setCellWidth ( width );
+ viewer.setCellHeight( height );
+ }
+
+ rowHeaders.setFixedCellHeight( viewer.getCellHeight() );
+ ruler.setPreferredWidthPerBase( viewer.getCellWidth() );
+ invalidate();
+ }
+
+ public void propertyChange( PropertyChangeEvent pce )
+ {
+ if( pce.getPropertyName().equals( "cellHeight" ) ){
+
+ int newValue = ((Integer)pce.getNewValue()).intValue();
+
+ rowHeaders.setFixedCellHeight( newValue );
+ rowHeaders.invalidate();
+ validate();
+ repaint();
+ }
+
+ if( pce.getPropertyName().equals( "cellWidth" ) ){
+
+ int newValue = ((Integer)pce.getNewValue()).intValue();
+
+ ruler.invalidate();
+ ruler.setPreferredWidthPerBase( newValue );
+ validate();
+ repaint();
+ }
+ }
+
+ //getters and setters
+ public void setSequenceAlignment( SequenceAlignment alignment )
+ {
+ viewer.setSequenceAlignment( alignment );
+ ruler.setSequenceAlignment( alignment );
+ rowHeaders.setSequenceAlignment( alignment );
+
+ Dictionary dic = ruler.getLabelTable();
+ JLabel oneLabel = (JLabel)dic.get( new Integer( 1 ) );
+ oneLabel.setText( " 1" );
+ ruler.setLabelTable( dic );
+ }
+
+
+ public JPanel getMainPanel()
+ {
+ return mainPanel;
+ }
+
+ public JAlignmentButtonPanel getRowHeaders()
+ {
+ return rowHeaders;
+ }
+
+ public JScrollPane getScrollPane()
+ {
+ return scrollPane;
+ }
+
+ public JPanel getRulerPanel()
+ {
+ return rulerPanel;
+ }
+
+ public JAlignmentViewer getViewer()
+ {
+ return viewer;
+ }
+
+ public JAlignmentRuler getRuler()
+ {
+ return ruler;
+ }
+
+ private void enableScrollPanePerformance( JViewport viewport )
+ {
+ // viewport.setBackingStoreEnabled( true );
+ viewport.putClientProperty
+ ( "EnableWindowBlot", Boolean.TRUE);
+ }
+
+ public void setOptions( Object opts )
+ {
+ super.setOptions( opts );
+
+ try{
+ HashMap options = (HashMap)opts;
+ if( options == null ) return;
+
+ Dimension dim = (Dimension)options.get( "cellSize" );
+
+ // if we have completed instantiation set the size.
+ if( viewer != null && dim != null ){
+ int width = (int)dim.getWidth();
+ int height = (int)dim.getHeight();
+ viewer.setCellWidth( (int)dim.getWidth() );
+ viewer.setCellHeight( (int)dim.getHeight() );
+ rowHeaders.setFixedCellHeight( height );
+ ruler.setPreferredWidthPerBase( width );
+ }
+ // if we have not, then store it for later.
+ else{
+ initialCellSize = dim;
+ }
+ }
+ catch( ClassCastException cce ){
+ // ignore. Should only occur during development or after version
+ // changes.
+ }
+ }
+
+ public Object getOptions()
+ {
+ HashMap options = (HashMap)super.getOptions();
+ if( viewer != null ){
+ options.put( "cellSize", new Dimension( viewer.getCellWidth(),
+ viewer.getCellHeight() ) );
+ }
+ return options;
+ }
+
+ public void dispose()
+ {
+ super.dispose();
+ mainPanel = rulerPanel = rowHeadersPanel = null;
+ viewer = null;
+ scrollPane = null;
+ rowHeaders = null;
+ ruler = null;
+ }
+
+} // CinemaAlignmentFrame
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaAlignmentFrame.java,v $
+ * Revision 1.12 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.11 2001/03/24 19:26:41 lord
+ * Null check when getting options prevents crash if frame has been
+ * killed by the user.
+ *
+ * Revision 1.10 2001/02/19 17:19:33 lord
+ * Made optionable
+ *
+ * Revision 1.9 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.8 2000/11/02 14:48:20 jns
+ * o added border as a tempory messure to the ruler pane. This will
+ * provide a bit of a gap between the JAV and the ruler stuff.
+ *
+ * Revision 1.7 2000/10/19 17:45:03 lord
+ * Removed some nasty debug code
+ *
+ * Revision 1.6 2000/09/27 16:21:04 jns
+ * o reverted back to single fast cell renderer, because of the ability
+ * to generate a multiplexer cell renderer that will render multiple cell
+ * renderers at one time.
+ *
+ * Revision 1.5 2000/09/18 17:54:00 jns
+ * o made to use the new multiplexer renderer rather than the default
+ *
+ * Revision 1.4 2000/09/15 17:32:28 lord
+ * Now destroyable.
+ * Most of the stuff in this function was added paranoically when I was
+ * trying to hunt a memory leak. It would probably GC correctly
+ * anyway. Still they do not hurt.
+ *
+ * Revision 1.3 2000/08/01 17:10:37 lord
+ * Now listens to height and width changes, and updates row headers and
+ * ruler appropriately
+ *
+ * Revision 1.2 2000/07/18 11:06:42 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/06/27 15:56:36 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.java
new file mode 100644
index 0000000..ac0466b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaDebug.java
@@ -0,0 +1,324 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import javax.swing.ButtonGroup;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingUtilities;
+import uk.ac.man.bioinf.apps.invoker.Invoker;
+import uk.ac.man.bioinf.debug.AbstractDebug;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.debug.DebugInterface;
+import uk.ac.man.bioinf.debug.DebugMultiplexer;
+import uk.ac.man.bioinf.debug.DefaultDebug;
+import uk.ac.man.bioinf.debug.DefaultFileDebug;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaDebug.java
+ *
+ * This class provides the Debugging architecture implementation for
+ * Cinema. It provides a Console GUI, files logs and oh so much more...
+ *
+ * Eventually the initial state of this should result from the XML
+ * initiation, but at the moment it just does lots of things at once.
+ *
+ * Created: Sun May 7 18:36:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaDebug.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaDebug extends Module implements ActionListener
+{
+ private DebugImpl dImpl = new DebugImpl();
+ private DebugInterface standardOutInterface, fileOutInterface;
+
+ private JFrame frame;
+ private JTextArea area;
+ private JMenuItem standardOutOn, standardOutOff, dumpToStandardOut;
+ private JMenuItem fileOutOn, fileOutOff, dumpToFile;
+
+ public void load()
+ {
+ Debug.message( this, "Cinema Debug: Load" );
+
+ // do the gui. Eventually this should be done only if the config
+ // information says to....
+ frame = new JFrame( "Cinema Debug Console" );
+ // basic console
+ area = new JTextArea();
+ JScrollPane scroll = new JScrollPane( area );
+ frame.getContentPane().add( scroll );
+
+ // menu bar
+ JMenuBar mb = new JMenuBar();
+ frame.setJMenuBar( mb );
+ JMenu options = new JMenu( "Options" );
+ mb.add( options );
+
+ // standard out tracing
+ ButtonGroup standardOut = new ButtonGroup();
+ standardOutOn = new JRadioButtonMenuItem( "Trace to stout" );
+ standardOutOn.addActionListener( this );
+ standardOut.add( standardOutOn );
+ options.add( standardOutOn );
+ standardOutOff = new JRadioButtonMenuItem( "No trace to stout" );
+ standardOutOff.addActionListener( this );
+ standardOut.add( standardOutOff );
+ standardOut.setSelected( standardOutOff.getModel(), true );
+ options.add( standardOutOff );
+
+ // standard out dump
+ dumpToStandardOut = new JMenuItem( "Dump contents to stout" );
+ dumpToStandardOut.addActionListener( this );
+ options.add( dumpToStandardOut );
+ options.addSeparator();
+
+ // file dumping gui controls
+ ButtonGroup fileOut = new ButtonGroup();
+ fileOutOn = new JRadioButtonMenuItem( "Trace to file" );
+ fileOutOn.addActionListener( this );
+ fileOut.add( fileOutOn );
+ options.add( fileOutOn );
+ fileOutOff = new JRadioButtonMenuItem( "No trace to file" );
+ fileOutOff.addActionListener( this );
+ fileOut.add( fileOutOff );
+ fileOut.setSelected( fileOutOff.getModel(), true );
+ options.add( fileOutOff );
+
+ // file out dump
+ dumpToFile = new JMenuItem( "Dump contents to file" );
+ dumpToFile.addActionListener( this );
+ options.add( dumpToFile );
+ }
+
+ public void start()
+ {
+ Debug.message( this, "Cinema Debug: Start" );
+ frame.setSize( 200, 400 );
+ frame.setVisible( true );
+
+ // install into the Debug architecture
+ DebugMultiplexer.addDebugInstance
+ ( dImpl );
+ DebugMultiplexer.addDebugInstance
+ ( standardOutInterface = new DefaultDebug() );
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ if( event.getSource() == standardOutOff && standardOutInterface != null ){
+ DebugMultiplexer.removeDebugInstance( standardOutInterface );
+ standardOutInterface = null;
+ }
+
+ if( event.getSource() == standardOutOn && standardOutInterface == null ){
+ DebugMultiplexer.addDebugInstance( standardOutInterface = new DefaultDebug() );
+ }
+
+ if( event.getSource() == dumpToStandardOut ){
+ System.out.println( "\nCinema Debug Console: Dumping to standard out\n" );
+ System.out.println( area.getText() );
+ System.out.println( "Cinema Debug Console: Dump to standard out complete\n" );
+ }
+
+ if( event.getSource() == fileOutOn ){
+ File file = selectWriteFile();
+
+
+ try{
+ if( file != null ){
+ if( fileOutInterface != null ){
+ DebugMultiplexer.removeDebugInstance( fileOutInterface );
+ }
+ if( Debug.debug ){
+ Debug.message( this, "Installing debug tracing to " + file );
+ }
+ DebugMultiplexer.addDebugInstance
+ ( fileOutInterface = new DefaultFileDebug( file ) );
+ }
+ }
+ catch( IOException io ){
+ // (PENDING:- PL) Need to have something better here, once I
+ // have generic method for informing the user of problems,
+ // which should probably be through the CinemaCoreView
+ if( Debug.debug ){
+ Debug.throwable( this, io );
+ }
+ }
+ }
+
+ if( event.getSource() == fileOutOff && fileOutInterface != null ){
+ DebugMultiplexer.removeDebugInstance( fileOutInterface );
+ fileOutInterface = null;
+ }
+
+ if( event.getSource() == dumpToFile ){
+ File file = selectWriteFile();
+ try{
+ if( file != null ){
+ PrintWriter write = new PrintWriter( new FileWriter( file ) );
+ write.println( area.getText() );
+ write.close();
+ }
+ }
+ catch( IOException io ){
+ if( Debug.debug ){
+ Debug.throwable( this, io );
+ }
+ }
+ }
+ }
+
+ private File selectWriteFile()
+ {
+ JFileChooser fileChooser = new JFileChooser();
+ int option = fileChooser.showSaveDialog( frame );
+ File chosenFile = fileChooser.getSelectedFile();
+
+ if( option == fileChooser.APPROVE_OPTION && chosenFile != null ){
+ return chosenFile;
+ }
+ return null;
+ }
+
+ public String getVersion()
+ {
+ return "$version: $";
+ }
+
+ private void message( Class cla, String message )
+ {
+ //defaultDeb.message( cla, message );
+ if( SwingUtilities.isEventDispatchThread() ){
+ area.append
+ ( formMessageString( message ) );
+ }else{
+ SwingUtilities.invokeLater
+ ( new Invoker( this, formMessageString( message ) )
+ {
+ public void doRun()
+ {
+ CinemaDebug.this.area.append( (String)getParameter() );
+ }
+ });
+ }
+ }
+
+ private String formMessageString( String message )
+ {
+ return "Debug Message: " + message + "\n";
+ }
+
+ private void throwable( Class cla, Throwable th )
+ {
+ //defaultDeb.throwable( cla, th );
+ if( SwingUtilities.isEventDispatchThread() ){
+ area.append( formStackTraceString( th ) );
+ }else{
+ // (PENDING:- PL) Theres a difficulty here. This should really
+ // be done with the CinemaInvoker module, because that will have
+ // the ExceptionHandler set. The difficult here is that the
+ // ExceptionHandler will probably go through this class, and so
+ // we have the first problem with which one to load first....
+ SwingUtilities.invokeLater
+ ( new Invoker( this, formStackTraceString( th ) )
+ {
+ public void doRun()
+ {
+ CinemaDebug.this.area.append( (String)getParameter() );
+ }
+ });
+ }
+ }
+
+ private String formStackTraceString( Throwable th )
+ {
+ StringWriter str = new StringWriter();
+ th.printStackTrace( new PrintWriter( str ) );
+ return
+ "Debug Throwable: " + th +
+ "Debug Stack: " + str.toString() + "\n";
+ }
+
+ public class DebugImpl extends AbstractDebug
+ {
+ public void message( Class cla, String message )
+ {
+ CinemaDebug.this.message( cla, message );
+ }
+
+ public void throwable( Class cla, Throwable th )
+ {
+ CinemaDebug.this.throwable( cla, th );
+ }
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaUtilityIdentifier.CINEMA_INVOKER );
+ return list;
+ }
+} // CinemaDebug
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaDebug.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/05/30 16:16:57 lord
+ * Import sorting, and module package completion
+ *
+ * Revision 1.2 2000/05/15 16:23:17 lord
+ * Reflecting changes in module method names
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.java
new file mode 100644
index 0000000..00731c8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaFileOptionableExceptionHandler.java
@@ -0,0 +1,139 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by Jde-Package
+import java.io.IOException;
+import javax.swing.JOptionPane;
+import uk.ac.man.bioinf.apps.optionable.OptionableExceptionHandler;
+import uk.ac.man.bioinf.apps.optionable.OptionableSourceNotFoundException;
+
+
+/**
+ * CinemaFileOptionableExceptionHandler.java
+ *
+ *
+ * Created: Mon May 14 16:21:58 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaFileOptionableExceptionHandler.java,v 1.2 2001/05/15 12:24:15 lord Exp $
+ */
+
+public class CinemaFileOptionableExceptionHandler implements OptionableExceptionHandler
+{
+ public boolean handleLoadException( Exception exp )
+ {
+ Object[] options =
+ { "Continue?", "Try Again?", "More Details?" };
+
+ int retn = JOptionPane.showOptionDialog
+ ( null, "<html>Warning:- There is some problem with restoring the settings. <p>" +
+ " Do you want to ", "Load error", JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[ 0 ] );
+
+ switch( retn )
+ {
+ case 0:
+ return false;
+ case 1:
+ return true;
+ case 2:
+ JOptionPane.showMessageDialog
+ ( null, "<html>Error reported as:<p> " + exp.getMessage(), "Error",
+ JOptionPane.INFORMATION_MESSAGE );
+ return handleLoadException( exp );
+ default:
+ // if this happens then something has gone badly wrong!
+ return false;
+ }
+ }
+
+ public boolean handleLoadException( IOException ioe )
+ {
+ return handleLoadException( (Exception)ioe );
+ }
+
+ public boolean handleLoadException( ClassNotFoundException exp )
+ {
+ // this should really only occur during development, or if the
+ // system has been inappropriately installed. The best course of
+ // action is just to report the error and move on.
+ Object[] options =
+ { "Ok", "More details" };
+
+ int retn = JOptionPane.showOptionDialog
+ ( null, "Warning:- Settings can not be restored. Using default options", "Warning",
+ JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[ 0 ] );
+
+ if( retn == 1 ){
+ JOptionPane.showMessageDialog
+ ( null, "<html>Error reported as: <p>" + exp.getMessage(), "Error",
+ JOptionPane.INFORMATION_MESSAGE );
+ }
+
+ // don't bother trying again.
+ return false;
+ }
+
+ public boolean handleLoadException( OptionableSourceNotFoundException osnfe )
+ {
+ // we can just ignore this. It probably means this is the first
+ // time that the system has been run.
+ return false;
+ }
+
+ public boolean handleSaveException( Exception exp )
+ {
+ Object[] options =
+ { "Continue?", "Try Again?", "More Details?" };
+
+ int retn = JOptionPane.showOptionDialog
+ ( null, "<html>Warning:- There is some problem with saving the settings. <p>" +
+ " Do you want to ", "Save error", JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[ 0 ] );
+
+ switch( retn )
+ {
+ case 0:
+ return false;
+ case 1:
+ return true;
+ case 2:
+ JOptionPane.showMessageDialog
+ ( null, "Error reported as: " + exp.getMessage(), "Error",
+ JOptionPane.INFORMATION_MESSAGE );
+ return handleSaveException( exp );
+ default:
+ // if this happens then something has gone badly wrong!
+ return false;
+ }
+ }
+
+ public boolean handleSaveException( IOException iop )
+ {
+ return handleSaveException( (Exception)iop );
+ }
+
+} // CinemaFileOptionableExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaFileOptionableExceptionHandler.java,v $
+ * Revision 1.2 2001/05/15 12:24:15 lord
+ * Added <html> tags to get the <p> tags to work properly.
+ *
+ * Revision 1.1 2001/05/14 17:08:18 lord
+ * Added proper error handling to save and restore.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.java
new file mode 100644
index 0000000..ccc9d10
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaFilePersist.java
@@ -0,0 +1,105 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.io.File;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents;
+import uk.ac.man.bioinf.apps.cinema.resources.CinemaResources;
+import uk.ac.man.bioinf.apps.optionable.FileSaveableOptions;
+import uk.ac.man.bioinf.apps.optionable.OptionHandler;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.util.ExceptionHandler;
+
+
+/**
+ * CinemaFilePersist.java
+ *
+ *
+ * Created: Tue Jan 30 15:53:21 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaFilePersist.java,v 1.4 2001/05/14 17:08:18 lord Exp $
+ */
+
+public class CinemaFilePersist extends CinemaPersist
+{
+ private OptionHandler optionHandler;
+
+ public void start()
+ {
+ File userPersist = CinemaResources.getUserPersist();
+
+ CinemaSystemEvents events = ((CinemaSystemEvents)getRequiredModule
+ ( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS ));
+
+ // (PENDING:- PL) This could do with improving.
+ CinemaFileOptionableExceptionHandler exp = new CinemaFileOptionableExceptionHandler();
+
+ optionHandler = new FileSaveableOptions
+ ( userPersist, events, exp );
+
+ super.start();
+ }
+
+ public OptionHandler getOptionHandler()
+ {
+ return optionHandler;
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaFilePersist.java,v 1.4 2001/05/14 17:08:18 lord Exp $";
+ }
+} // CinemaFilePersist
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaFilePersist.java,v $
+ * Revision 1.4 2001/05/14 17:08:18 lord
+ * Added proper error handling to save and restore.
+ *
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/02/19 17:20:05 lord
+ * Added super call
+ *
+ * Revision 1.1 2001/01/31 17:51:40 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.java
new file mode 100644
index 0000000..5cbc406
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaInvoker.java
@@ -0,0 +1,107 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.cinema.core.CinemaCoreIdentifier;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaSystemEvents;
+import uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+
+
+/**
+ * CinemaInvoker.java
+ *
+ *
+ * Created: Tue Apr 25 20:24:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaInvoker.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaInvoker extends Module
+{
+ private InvokerInternalQueue qu;
+
+ public void start()
+ {
+ qu = getNewInvokerInternalQueue();
+ }
+
+ public InvokerInternalQueue getInvokerInternalQueue()
+ {
+ return qu;
+ }
+
+ public InvokerInternalQueue getNewInvokerInternalQueue()
+ {
+ return new InvokerInternalQueue( getCinemaSystemEvents() );
+ }
+
+ private CinemaSystemEvents getCinemaSystemEvents()
+ {
+ return (CinemaSystemEvents)getRequiredModule( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaInvoker.java,v 1.4 2001/04/11 17:04:42 lord Exp $";
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaCoreIdentifier.CINEMA_SYSTEM_EVENTS );
+ return list;
+ }
+
+} // CinemaInvoker
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaInvoker.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/05/30 16:18:44 lord
+ * Removed identifier to CinemaUtilityIdentifier. Import sorting.
+ * Module package completion
+ *
+ * Revision 1.2 2000/05/24 15:37:39 lord
+ * Updated for change in ModuleInterface interface
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ */
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.java
new file mode 100644
index 0000000..ed6239c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaMenuBuilder.java
@@ -0,0 +1,181 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import javax.swing.Action;
+import javax.swing.JMenu;
+import javax.swing.JMenuBar;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaActionProvider;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaAlignmentFrame;
+import uk.ac.man.bioinf.apps.xml.ConfigNode;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.ModuleException;
+
+
+/**
+ * CinemaMenuBuilder.java
+ *
+ * This class builds a menu system based upon the module configuration
+ * information.
+ * The format of the config info should look something like this...
+ *
+ * <code>
+ * <pre>
+ * <!-- The File Menu -->
+ *
+ * <node>
+ * <value>File</value>
+ * <node>
+ * <!-- Provides the open alignment -->
+ * <name>SEQ_INPUT</name>
+ * </node>
+ * <node>
+ * <!-- Provides the save alignment -->
+ * <name>SEQ_OUTPUT</name>
+ * </node>
+ * </node>
+ *
+ * <!-- The Colour Selector -->
+ * <node>
+ * <value>Colour Selector</value>
+ * <node>
+ * <name>CINEMA_COLOR_SELECTOR</name>
+ * </node>
+ * </node>
+ * </node>
+ * </pre>
+ * </code>
+ *
+ * Essentially a "Value" is translated as the title of a menu whilst
+ * "name" is translated as a Module which will provide actions for
+ * that menu. This makes arbitrarily deep menu systems to be
+ * constructed.
+ *
+ * Created: Fri Oct 13 15:26:26 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaMenuBuilder.java,v 1.5 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaMenuBuilder extends CinemaModule
+{
+ /**
+ * This is the build method. The ConfigNode should be the root nodes
+ * which describe the menu system.
+ * @param frame this is optional and can be null. If it is present
+ * then it will be passed to those menu items which require it.
+ * @param menuBar this is the JMenuBar to use.
+ * @param mainMenuItems this are there configuration nodes which
+ * describe the menu system.
+ */
+ public void buildMenu( CinemaAlignmentFrame frame, JMenuBar menuBar, ConfigNode[] mainMenuItems )
+ {
+ //add the main menu items
+ for( int i = 0; i < mainMenuItems.length; i++ ){
+ JMenu menu = new JMenu( mainMenuItems[ i ].getStringData() );
+ menuBar.add( menu );
+ addToMenu( frame, menu, mainMenuItems[ i ] );
+ }
+ }
+
+ private void addToMenu( CinemaAlignmentFrame frame, JMenu menu, ConfigNode node )
+ {
+ ConfigNode[] childNode = node.getChildNodes();
+ for( int i = 0; i < childNode.length; i++ ){
+ if( !childNode[ i ].isModuleIdentifier() ){
+ // this is not a module. So it a value which indicates a
+ // submenu. So make the menu, and add all children via a
+ // recursive call
+ JMenu childMenu = new JMenu( childNode[ i ].getStringData() );
+ menu.add( childMenu );
+ addToMenu( frame, childMenu, childNode[ i ] );
+ }
+ else{
+ // we have a module. This module will implement
+ // CinemaActionProvider, and we can get actions from this.
+ // (PENDING:- PL) I do not like this. The ConfigNode should be
+ // able to return a Module directly, rather than a String
+ try{
+
+ Object prov = getContext().getModule( childNode[ i ].getModuleData() );
+
+ // fetch the actions, passing in the AlignmentFrame if necessary
+ Action[] actions;
+ // I don't like this code at all. Its seems a bit of a hack.
+ if( prov instanceof CinemaFramedActionProvider ){
+ actions = ((CinemaFramedActionProvider)prov).getActions( frame );
+ }
+ else{
+ actions = ((CinemaActionProvider)prov).getActions();
+ }
+
+ // add them to the menu bar
+ for( int j = 0; j < actions.length; j++ ){
+ menu.add( actions[ j ] );
+ }
+ }
+ catch( ModuleException me ){
+ me.printStackTrace();
+
+ if( Debug.debug )
+ Debug.throwable( this, me );
+ }
+ }
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaMenuBuilder.java,v 1.5 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaMenuBuilder
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaMenuBuilder.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2001/01/31 18:06:22 lord
+ * Improved exception handling.
+ *
+ * Revision 1.3 2000/12/18 12:12:22 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.2 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/10/19 17:45:42 lord
+ * Initial checkin. Most of this code came previously from CinemaMenuSystem
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.java
new file mode 100644
index 0000000..0811665
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaMultipleConsensusViewer.java
@@ -0,0 +1,205 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.CinemaProperties;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder;
+import uk.ac.man.bioinf.apps.cinema.utils.CinemaUtilityIdentifier;
+import uk.ac.man.bioinf.apps.xml.ConfigNode;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.gui.viewer.ButtonViewerPopupMenu;
+import uk.ac.man.bioinf.module.ModuleIdentifierList;
+import uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * CinemaMultipleConsensusViewer.java
+ *
+ *
+ * Created: Fri Jun 23 12:09:24 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaMultipleConsensusViewer.java,v 1.7 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaMultipleConsensusViewer extends CinemaModule
+ implements PropertyChangeListener, ActionListener
+{
+ private CinemaAlignmentFrame alignmentFrame;
+ private SequenceAlignment alignmentGroup;
+ private JMenuItem clearElements, removeSequence;
+ private ButtonViewerPopupMenu buttonPopup;
+
+ public void load()
+ {
+ // (PENDING:- PL) This sequence type should not be hard coded in here!
+ alignmentGroup = new DefaultSequenceAlignment( ProteinSequenceType.getInstance() );
+ alignmentFrame = new CinemaAlignmentFrame( "cinema.utils.multiple.consensus",
+ "Cinema Multiple Consensus Viewer", alignmentGroup );
+
+ ConsensusPercentageIDColorMap colorMap = new ConsensusPercentageIDColorMap( alignmentGroup );
+ buttonPopup = new ButtonViewerPopupMenu( alignmentFrame.getRowHeaders() );
+
+ removeSequence = new JMenuItem( "Remove Sequence" );
+ removeSequence.addActionListener( this );
+ buttonPopup.add( removeSequence );
+
+ alignmentFrame.getViewer().setColorMap( colorMap );
+ alignmentFrame.setDefaultSize( 300, 300 );
+ }
+
+ public void start()
+ {
+ JMenuBar menuBar = alignmentFrame.getJMenuBar();
+ ConfigNode[] mainMenuItems = getConfigTree().getChildNodes();
+ CinemaMenuBuilder builder = (CinemaMenuBuilder)getRequiredModule
+ ( CinemaUtilityIdentifier.CINEMA_MENU_BUILDER );
+ builder.buildMenu( alignmentFrame, menuBar, mainMenuItems );
+
+ addCinemaPropertyChangeListener( CinemaProperties.SEQ_ALIGN.toString(),
+ this );
+ }
+
+ public void addConsensusSequence( ConsensusSequence sequence )
+ {
+ alignmentFrame.setVisible( true );
+ try {
+ alignmentGroup.addSequence( sequence, 0 );
+ } catch (AlignmentVetoException e) {
+ /* (PENDING: JNS) 25.10.00 going to do what PL did and just
+ * ignore this exception for the mo. It will need dealing with.
+ */
+ Debug.both(this, "Cinema Multiple Consensus Viewer: " +
+ "Cannot add consensus sequence because of a veto", e);
+ }
+ }
+
+ public void removeConsensusSequence( ConsensusSequence sequence )
+ {
+ try {
+ alignmentGroup.removeSequence( alignmentGroup.getSequenceIndex(sequence) );
+ } catch (AlignmentVetoException e) {
+ /* (PENDING: JNS) 25.10.00 going to do what PL did and just
+ * ignore this exception for the mo. It will need dealing with.
+ */
+ Debug.both(this, "Cinema Multiple Consensus Viewer: " +
+ "Cannot remove consensus sequence because of a veto", e);
+ }
+ }
+
+ public void destroy()
+ {
+ alignmentFrame.dispose();
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ if( event.getSource() == removeSequence ){
+ try {
+ alignmentGroup.removeSequence
+ ( alignmentGroup.getSequenceIndex(buttonPopup.getSelectedSequence()) );
+ } catch (AlignmentVetoException e) {
+ /* (PENDING: JNS) 25.10.00 going to do what PL did and just
+ * ignore this exception for the mo. It will need dealing with.
+ */
+ Debug.both(this, "Cinema Multiple Consensus Viewer: " +
+ "Cannot add consensus sequence", e);
+ }
+ }
+ }
+
+ public void propertyChange( PropertyChangeEvent evt )
+ {
+ if( evt.getPropertyName().equals( CinemaProperties.SEQ_ALIGN.toString() ) ){
+ // remove all sequences from the group
+ for (int i = 0; i < alignmentGroup.getNumberSequences(); i++)
+ try {
+ alignmentGroup.removeSequence(i);
+ } catch (AlignmentVetoException e) {
+ /* (PENDING: JNS) 25.10.00 going to do what PL did and just
+ * ignore this exception for the mo. It will need dealing with.
+ */
+ Debug.both(this, "Cinema Multiple Consensus Viewer: " +
+ "Cannot add consensus sequence", e);
+ }
+ }
+ }
+
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ ModuleIdentifierList list = super.getRequiredIdentifiers();
+ list.add( CinemaUtilityIdentifier.CINEMA_MENU_BUILDER );
+ return list;
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaMultipleConsensusViewer.java,v 1.7 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaMultipleConsensusViewer
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaMultipleConsensusViewer.java,v $
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/02/19 17:20:22 lord
+ * Made optionable
+ *
+ * Revision 1.5 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.4 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.3 2000/10/19 17:46:09 lord
+ * Some event handling. Remove sequence button added.
+ *
+ * Revision 1.2 2000/09/15 17:32:55 lord
+ * Now destroyable
+ *
+ * Revision 1.1 2000/06/27 15:56:36 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.java
new file mode 100644
index 0000000..57c4508
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaPersist.java
@@ -0,0 +1,75 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.optionable.OptionHandler;
+import uk.ac.man.bioinf.gui.optionable.OptionableJFrame;
+import uk.ac.man.bioinf.gui.optionable.OptionableJSplitPane;
+
+
+/**
+ * CinemaPersist.java
+ *
+ * Provides the OptionHandler which classes need to implement persistance.
+ * Created: Tue Jan 30 15:31:24 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaPersist.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class CinemaPersist extends CinemaModule
+{
+ public void start()
+ {
+ super.start();
+
+ // (PENDING:- PL) Need to put in support here for all the
+ // libraries that automatically require this.
+ OptionableJFrame.setDefaultOptionHandler( getOptionHandler() );
+ OptionableJSplitPane.setDefaultOptionHandler( getOptionHandler() );
+ }
+
+ public abstract OptionHandler getOptionHandler();
+} // CinemaPersist
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaPersist.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/03/12 16:46:51 lord
+ * Added support for more libraries.
+ *
+ * Revision 1.1 2001/01/31 17:51:40 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.java
new file mode 100644
index 0000000..81d4690
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaRegexp.java
@@ -0,0 +1,166 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.awt.event.ActionEvent;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.JOptionPane;
+import org.apache.regexp.RE;
+import org.apache.regexp.RECompiler;
+import org.apache.regexp.RESyntaxException;
+import uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * CinemaRegexp.java
+ *
+ * Provides support for various regexp searching facilities.
+ *
+ * Created: Fri Feb 9 11:38:52 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaRegexp.java,v 1.4 2001/05/22 16:03:01 lord Exp $
+ */
+
+public class CinemaRegexp extends CinemaModule
+ implements CinemaFramedActionProvider
+{
+ private RE regexp = new RE();
+ private RECompiler compiler = new RECompiler();
+
+ private void searchForward( String regex, CinemaAlignmentFrame frame )
+ {
+ try{
+ // first get the sequence at point
+ JAlignmentViewer viewer = frame.getViewer();
+ SequenceAlignmentPoint point = viewer.getPoint();
+
+ GappedSequence seq = viewer.getSequenceAlignment().
+ getSequenceAt( point.getY() );
+
+ // now construct the regexp that we need.
+ regexp.setProgram( compiler.compile( regex ) );
+
+ SequenceCharacterIterator iter = new SequenceCharacterIterator( seq );
+
+ int startPos = point.getX() - viewer.getSequenceAlignment().getInset( point.getY() ) + 1;
+ startPos = ((startPos < 0 ) ? startPos = 0: seq.getUngappedPositionOf( startPos ) );
+
+ if( regexp.match( iter, startPos ) ){
+
+ SequenceAlignmentPoint startPoint = new SequenceAlignmentPoint( point );
+ SequenceAlignmentPoint endPoint = new SequenceAlignmentPoint( point );
+
+ startPoint.setX( seq.getGappedPositionOf( regexp.getParenStart( 0 ) + 1 ) +
+ viewer.getSequenceAlignment().getInset( point.getY() ) );
+
+ endPoint.setX( ( seq.getGappedPositionOf( regexp.getParenEnd( 0 ) + 1 ) +
+ viewer.getSequenceAlignment().getInset( point.getY() ) ) );
+
+ viewer.ensureSequencePointIsVisible( endPoint );
+ viewer.ensureSequencePointIsVisible( startPoint );
+ viewer.moveCursorToSequencePoint( startPoint );
+ }
+ else{
+ JOptionPane.showMessageDialog(null, "The search term could not be found", "Not Found",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ catch( RESyntaxException rese ){
+ JOptionPane.showMessageDialog(null, "The regular expression you entered is invalid","Invalid regexp",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ }
+
+ public Action[] getActions( CinemaAlignmentFrame frame )
+ {
+ Action[] retn = new Action[ 1 ];
+ retn[ 0 ] = new FramedAbstractAction( frame, "Search Forward" ){
+ private String lastRegexp;
+
+ public void actionPerformed( ActionEvent event )
+ {
+ String search = (String)JOptionPane.showInputDialog
+ ( getAlignmentFrame(), "Regexp Search Forward", "Re-search forward",
+ JOptionPane.QUESTION_MESSAGE, null, null, lastRegexp );
+ lastRegexp = search;
+
+ searchForward( search, getAlignmentFrame() );
+ }
+ };
+ return retn;
+ }
+
+ abstract class FramedAbstractAction extends AbstractAction
+ {
+ private CinemaAlignmentFrame frame;
+
+ FramedAbstractAction( CinemaAlignmentFrame frame, String title )
+ {
+ super( title );
+ this.frame = frame;
+ }
+
+ CinemaAlignmentFrame getAlignmentFrame()
+ {
+ return frame;
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaRegexp.java,v 1.4 2001/05/22 16:03:01 lord Exp $";
+ }
+
+} // CinemaRegexp
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaRegexp.java,v $
+ * Revision 1.4 2001/05/22 16:03:01 lord
+ * Lots of numbers and off by one errors have been fixed.
+ *
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/03/12 16:47:07 lord
+ * Removed debug
+ *
+ * Revision 1.1 2001/02/19 17:20:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.java
new file mode 100644
index 0000000..ea65698
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaResizeElements.java
@@ -0,0 +1,385 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.HashMap;
+import javax.swing.AbstractAction;
+import javax.swing.Action;
+import javax.swing.BoxLayout;
+import javax.swing.JCheckBox;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.core.CinemaFramedActionProvider;
+import uk.ac.man.bioinf.gui.optionable.OptionableJFrame;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+
+
+/**
+ * CinemaResizeElements.java
+ *
+ *
+ * Created: Wed Jul 26 14:40:14 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaResizeElements.java,v 1.9 2001/07/06 12:51:58 lord Exp $
+ */
+
+public class CinemaResizeElements extends CinemaModule
+ implements CinemaFramedActionProvider
+{
+
+ public Action[] getActions( CinemaAlignmentFrame frame )
+ {
+ return new Action[]{
+ new FramedAbstractAction( frame, "Resize Elements" )
+ };
+ }
+
+ class FramedAbstractAction extends AbstractAction
+ {
+ private CinemaAlignmentFrame frame;
+ private ResizerGui gui;
+
+ FramedAbstractAction( CinemaAlignmentFrame frame, String title )
+ {
+ super( title );
+ this.frame = frame;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ // if there is no instance of the re-sizer, create one
+ if( gui == null ){
+ gui = new ResizerGui( frame );
+ }
+
+ // set the gui visible, if it isn't already
+ if (! gui.isVisible())
+ gui.setVisible( true );
+
+ // if the gui is minimized then pop it up
+ if (gui.getState() == Frame.ICONIFIED)
+ gui.setState(Frame.NORMAL);
+
+ // bring the gui to the front
+ gui.toFront();
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: ";
+ }
+
+ // this is a nasty hack. I need to work out whether I am using a JVM
+ // which is suffering from the bug described in bug parade 4246117,
+ // which makes the GUI malfunction. This provides a work around. The
+ // GUI is not as pretty as it should be but it works.
+ private static boolean isValueAdjustingBuggyJVM;
+ static
+ {
+ String vendor = System.getProperty( "java.vendor" );
+ String version = System.getProperty( "java.version" );
+
+ if( vendor.equals( "Sun Microsystems Inc." ) &&
+ version.startsWith( "1.2.2" ) ){
+ isValueAdjustingBuggyJVM = true;
+ }
+ }
+
+ class ResizerGui extends OptionableJFrame implements ChangeListener, ActionListener
+ {
+ private JSlider xSizeSlider;
+ private JSlider ySizeSlider;
+ private JPanel elementSizeComponent;
+ private JCheckBox square, aspect;
+ private double aspectRatio;
+
+ private CinemaAlignmentFrame alignFrame;
+
+ public ResizerGui( CinemaAlignmentFrame alignFrame )
+ {
+ super( "utils.resizer.gui." + alignFrame.getTitle(),
+ "Set Cell Size:- " + alignFrame.getTitle(), true );
+
+ this.alignFrame = alignFrame;
+
+ //This is the main container panel
+ JPanel elementSizeChooserPanel = new JPanel();
+ elementSizeChooserPanel.setLayout( new BorderLayout() );
+
+ JAlignmentViewer view = alignFrame.getViewer();
+ int elementWidth = view.getCellWidth();
+ int elementHeight = view.getCellHeight();
+
+
+ //Heres the slider and label set up
+ JPanel sliderAndLabelPanel = new JPanel();
+ sliderAndLabelPanel.setLayout( new BoxLayout( sliderAndLabelPanel, BoxLayout.Y_AXIS ) );
+
+ // controls the X axis
+ JLabel sliderLabel = new JLabel( "Width" );
+ xSizeSlider = new JSlider( 1, 85, elementWidth );
+ xSizeSlider.addChangeListener( this );
+ xSizeSlider.setPaintTicks( true );
+ xSizeSlider.setPaintLabels( true );
+ xSizeSlider.setMajorTickSpacing( 20 );
+ xSizeSlider.setMinorTickSpacing( 4 );
+ sliderAndLabelPanel.add( sliderLabel );
+ sliderAndLabelPanel.add( xSizeSlider );
+
+ // controls the Y axis
+ sliderLabel = new JLabel( "Height" );
+ ySizeSlider = new JSlider( 1, 85, elementHeight );
+ ySizeSlider.addChangeListener( this );
+ ySizeSlider.setPaintTicks( true );
+ ySizeSlider.setPaintLabels( true );
+ ySizeSlider.setMajorTickSpacing( 20 );
+ ySizeSlider.setMinorTickSpacing( 4 );
+ sliderAndLabelPanel.add( sliderLabel );
+ sliderAndLabelPanel.add( ySizeSlider );
+
+ JPanel buttonPanel = new JPanel();
+ // keep square. Which switch this ON by default latter in the
+ // constructor.
+ square = new JCheckBox( "Keep Square" );
+
+ aspect = new JCheckBox( "Maintain aspect" );
+ square.addActionListener( this );
+ aspect.addActionListener( this );
+ buttonPanel.add( square );
+ buttonPanel.add( aspect );
+ sliderAndLabelPanel.add( buttonPanel );
+
+
+ //This is the panel that resizes to show the size of the thumb nails
+ elementSizeComponent = new JPanel();
+ elementSizeComponent.setBackground( Color.black );
+
+ elementSizeComponent.setSize( elementWidth, elementHeight );
+ elementSizeComponent.setLocation( new Point( 0, 0 ) );
+ //This panel is invisible and it within this panel that the coloured
+ //size panel changes
+ JPanel outerElementPanel = new JPanel();
+ //we want to specify the contents here specifically
+ outerElementPanel.setLayout( null );
+ outerElementPanel.setPreferredSize( new Dimension( 98, 140 ) );
+ outerElementPanel.add( elementSizeComponent );
+
+ elementSizeChooserPanel.add( sliderAndLabelPanel, BorderLayout.CENTER );
+ elementSizeChooserPanel.add( outerElementPanel, BorderLayout.EAST );
+
+ // make square selected by default
+ setIsSquare( true );
+
+ getContentPane().add( elementSizeChooserPanel );
+
+ pack();
+ forceOptionable();
+ setDefaultCloseOperation( JFrame.HIDE_ON_CLOSE );
+ }
+
+ public void actionPerformed( ActionEvent ae )
+ {
+ if( ae.getSource() == square ){
+ setIsSquare( square.isSelected() );
+ }
+
+ if( ae.getSource() == aspect ){
+ setMaintainAspect( aspect.isSelected() );
+ }
+ }
+
+ // implementation of javax.swing.event.ChangeListener interface
+ public void stateChanged( ChangeEvent event )
+ {
+ boolean xValueIsAdjusting = true;
+ xValueIsAdjusting = xSizeSlider.getModel().getValueIsAdjusting();
+ boolean yValueIsAdjusting = true;
+ yValueIsAdjusting = ySizeSlider.getModel().getValueIsAdjusting();
+
+ // there is a bug in Sun's 1.2.2 JVM's which means that JSlider
+ // always returns true for this value, at least when the slider
+ // is operated by the mouse. As this is quite a performance hit
+ // I have decided to make a JVM specific bug fix in this case
+ if( isValueAdjustingBuggyJVM ){
+ xValueIsAdjusting = yValueIsAdjusting = false;
+ }
+
+ if( event.getSource() == xSizeSlider ){
+ setElementXSize( xSizeSlider.getModel().getValue(),
+ xValueIsAdjusting );
+ }
+
+ if( event.getSource() == ySizeSlider ){
+ setElementYSize( ySizeSlider.getModel().getValue(),
+ yValueIsAdjusting );
+ }
+ }
+
+ private void setElementXSize( int value, boolean xValueIsAdjusting )
+ {
+ // if we are maintaining the aspect ratio then adjust ySlider
+ if( aspect.isSelected() ){
+ elementSizeComponent.setSize( value, (int)(value * aspectRatio) );
+ }
+ else{
+ elementSizeComponent.setSize( value, elementSizeComponent.getHeight() );
+ }
+
+ // if we have finished adjusting then send the adjust the viewer
+ if( !xValueIsAdjusting ){
+ if( aspect.isSelected() ){
+ alignFrame.getViewer().setCellHeight( (int)(value * aspectRatio) );
+ }
+ alignFrame.getViewer().setCellWidth( value );
+ }
+ }
+
+ private void setElementYSize( int value, boolean yValueIsAdjusting )
+ {
+ elementSizeComponent.setSize( elementSizeComponent.getWidth(), value );
+
+ if( !yValueIsAdjusting ){
+ alignFrame.getViewer().setCellHeight( value );
+ }
+ }
+
+ private void setMaintainAspect( boolean aspect )
+ {
+ this.aspect.setSelected( aspect );
+ if( aspect ){
+ ySizeSlider.setEnabled( false );
+ aspectRatio = (double)xSizeSlider.getModel().getValue()
+ / (double)ySizeSlider.getModel().getValue();
+ }
+ else{
+ ySizeSlider.setEnabled( true );
+ }
+ }
+
+ private void setIsSquare( boolean square )
+ {
+ this.square.setSelected( square );
+ if( square ){
+ // to make a square, seq y equal to x and maintain the aspect ratio
+ aspect.setSelected( true );
+ aspect.setEnabled( false );
+ ySizeSlider.setEnabled( false );
+ aspectRatio = 1;
+ }
+ else{
+ aspect.setEnabled( true );
+ ySizeSlider.setEnabled( true );
+ }
+ }
+
+
+ public Object getOptions()
+ {
+ HashMap options = (HashMap)super.getOptions();
+ options.put( "isAspect", new Boolean( aspect.isSelected() ) );
+ options.put( "isSquare", new Boolean( square.isSelected() ) );
+ return options;
+ }
+
+ public void setOptions( Object opts )
+ {
+ if( opts == null ) return;
+
+ try{
+ HashMap options = (HashMap)opts;
+ setMaintainAspect
+ ( ((Boolean)options.get( "isAspect" )).booleanValue() );
+ setIsSquare
+ ( ((Boolean)options.get( "isSquare" )).booleanValue() );
+ }
+ catch( ClassCastException cce ){
+ // ignore. Should only occur during development or after
+ // version changes
+ }
+ }
+ }
+
+ public static void main( String[] args )
+ {
+ CinemaResizeElements c = new CinemaResizeElements();
+ c.start();
+ } //end main method
+} // CinemaResizeElements
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaResizeElements.java,v $
+ * Revision 1.9 2001/07/06 12:51:58 lord
+ * Square by default
+ *
+ * Revision 1.8 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2001/02/19 17:21:13 lord
+ * Made optionable
+ *
+ * Revision 1.6 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.5 2000/11/02 16:10:37 jns
+ * o making sure that resize gui will appear each time it is called - it
+ * wasn't previously - bug fixed
+ *
+ * Revision 1.4 2000/10/19 17:47:52 lord
+ * Serious code shuffling. Most of the code is the same but its all
+ * been moved around. In particularly the GUI code is all in an inner
+ * class. This has the practical effect of allowing multiple instances of
+ * the Resizer.
+ *
+ * Revision 1.3 2000/08/22 16:25:50 lord
+ * Added some nasty hack code to work aroung JSlider bug
+ * specific to Sun's 1.2.2 JVM's.
+ *
+ * Revision 1.2 2000/08/02 14:52:51 lord
+ * Now provides menu item and responds to it correctly.
+ *
+ * Revision 1.1 2000/08/01 17:19:38 lord
+ * Intial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.java
new file mode 100644
index 0000000..39a16b1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaSlaveViewerModule.java
@@ -0,0 +1,126 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.apps.cinema.CinemaModule;
+import uk.ac.man.bioinf.apps.cinema.color.AminoAcidColorMapMetaData;
+import uk.ac.man.bioinf.apps.cinema.color.CinemaColorFactory;
+import uk.ac.man.bioinf.apps.cinema.color.CinemaColorIdentifier;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.module.ModuleContext;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * CinemaSlaveViewerModule.java
+ *
+ * Generates arbitrary numbers of Slave Viewers. At lot of the code
+ * here is very similar to that in CinemaCoreGui, and it would
+ * probably make sense to consolidate some of this into a single
+ * place.
+ *
+ * The point of a slave viewer is to show an alignment which is not
+ * the main alignment. It will not produce events like the main
+ * alignment, and will not control everything else. At the moment the
+ * main reason for writing this is so that I can test out some other
+ * data structures I have written but I think that this will be a
+ * useful functionality in the end.
+ *
+ * Created: Sun Jun 4 20:26:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaSlaveViewerModule.java,v 1.7 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaSlaveViewerModule extends CinemaModule
+{
+ public void showSlaveAlignment( SequenceAlignment alignment )
+ {
+ CinemaAlignmentFrame frame = new CinemaAlignmentFrame
+ ( "cinema.utils.slave.viewer", "Cinema Slave Viewer", alignment );
+ ModuleContext context = getContext();
+
+ if( context.isModuleAvailable( CinemaColorIdentifier.CINEMA_COLOR_FACTORY ) ){
+ try{
+ CinemaColorFactory fact = (CinemaColorFactory)context.getModule( CinemaColorIdentifier.CINEMA_COLOR_FACTORY );
+ ColorMap map = fact.getMetaData( AminoAcidColorMapMetaData.NAME ).
+ getInstance( getSequenceAlignment(), frame.getViewer() );
+ frame.getViewer().setColorMap( map );
+ }
+ catch( NullPointerException npe ){
+ }
+ catch( ModuleException me ){
+ // just ignore this, its not critical
+ }
+ }
+
+ frame.setDefaultSize( 200, 200 );
+ frame.setVisible( true );
+
+ }
+
+ //public ModuleIdentifierList get
+
+ public String getVersion()
+ {
+ return "$Id: CinemaSlaveViewerModule.java,v 1.7 2001/04/11 17:04:42 lord Exp $";
+ }
+} // CinemaSlaveViewerModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaSlaveViewerModule.java,v $
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/03/24 19:27:12 lord
+ * Added standard colour scheme if the relevant modules are
+ * available.
+ *
+ * Revision 1.5 2001/02/19 17:21:23 lord
+ * Made optionable
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/10/19 17:50:46 lord
+ * Does not require CinemaSequenceMenu any more, as this is really only
+ * useful for the main Cinema Viewer.
+ *
+ * Revision 1.2 2000/06/27 15:57:20 lord
+ * Now uses the CinemaAlignmentFrame, thereby rationalising the code
+ * in here, with that in the CinemaCoreGui
+ *
+ * Revision 1.1 2000/06/05 14:17:33 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.java
new file mode 100644
index 0000000..13aa9ff
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaStatusInformation.java
@@ -0,0 +1,181 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import java.beans.PropertyChangeListener;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import uk.ac.man.bioinf.apps.cinema.CinemaGuiModule;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import java.beans.PropertyChangeEvent;
+import uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel;
+import uk.ac.man.bioinf.gui.viewer.SequenceCursor;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment;
+
+
+/**
+ * CinemaStatusInformation.java
+ *
+ * A utility class which provides what are hopefully useful status bar
+ * information messages about what Cinema is currently showing.
+ *
+ * Created: Fri Jan 26 15:49:33 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaStatusInformation.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaStatusInformation extends CinemaGuiModule implements PropertyChangeListener
+{
+ public void start()
+ {
+
+ getViewer().addPropertyChangeListener( this );
+
+ addSelectionListener( null, getViewer().getSelectionModel() );
+ addCursorListener( null, getViewer().getCursorModel() );
+ printSequenceInfo();
+
+ }
+
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ if( event.getPropertyName().equals( "sequenceAlignment" ) ){
+ printSequenceInfo();
+ }
+
+ if( event.getPropertyName().equals( "alignmentSelectionModel" ) ){
+ addSelectionListener( (AlignmentSelectionModel)event.getOldValue(),
+ (AlignmentSelectionModel)event.getNewValue() );
+ }
+
+ if( event.getPropertyName().equals( "sequenceCursor" ) ){
+ addCursorListener( (SequenceCursor)event.getOldValue(),
+ (SequenceCursor)event.getNewValue() );
+ }
+ }
+
+ private void printSequenceInfo()
+ {
+ SequenceAlignment seq = getViewer().getSequenceAlignment();
+
+ if( !(seq instanceof EmptySequenceAlignment ) ){
+ sendStatusMessage
+ ( "Loaded " + seq.getIdentifier().getTitle() + " from " +
+ seq.getIdentifier().getSource().getTitle() );
+
+ Identifier identifier;
+ if( (identifier = seq.getIdentifier()) instanceof NoIdentifier ){
+ setFrameTitle( identifier.getSource().getTitle() );
+ }
+ else{
+ setFrameTitle( identifier.getTitle() );
+ }
+ }
+ }
+
+ private AlignmentSelectionListener selectionListener;
+
+ private void addSelectionListener( AlignmentSelectionModel oldMod, AlignmentSelectionModel newMod )
+ {
+ if( selectionListener == null ){
+ selectionListener = new AlignmentSelectionListener(){
+ public void valueChanged( AlignmentSelectionEvent event )
+ {
+ printSelectionInfo( event.getSelectionRectangle() );
+ }
+ };
+ }
+
+ if( oldMod != null ) oldMod.removeAlignmentSelectionListener( selectionListener );
+ if( newMod != null ) newMod.addAlignmentSelectionListener( selectionListener );
+ }
+
+ private void printSelectionInfo( SequenceAlignmentRectangle rect )
+ {
+ if( rect != null ){
+ sendStatusMessage
+ ( "Selection: ( " + rect.getX() + " , " + rect.getY() +
+ " - " + rect.getWidth() + " x " + rect.getHeight() + " )" ) ;
+ }
+ }
+
+ private ChangeListener cursorListener;
+
+ private void addCursorListener( SequenceCursor oldMod, SequenceCursor newMod )
+ {
+ if( cursorListener == null ){
+ cursorListener = new ChangeListener(){
+ public void stateChanged( ChangeEvent event )
+ {
+ printCursorInfo();
+ }
+ };
+ }
+
+ if( oldMod != null ) oldMod.removeChangeListener( cursorListener );
+ if( newMod != null ) newMod.addChangeListener( cursorListener );
+ }
+
+ private void printCursorInfo()
+ {
+ SequenceAlignmentPoint point = getViewer().getPoint();
+
+ sendStatusMessage
+ ( getSequenceAlignment().getIdentifier().getTitle() + " @ ( " + point.getX() + " , " +
+ point.getY() + " )" );
+ }
+
+ public String getVersion()
+ {
+ return "$Id: CinemaStatusInformation.java,v 1.3 2001/04/11 17:04:42 lord Exp $";
+ }
+
+}// CinemaStatusInformation
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaStatusInformation.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/27 17:08:33 lord
+ * Does not update title bar for EmptySequenceAlignment
+ *
+ * Revision 1.1 2001/01/27 16:56:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.java b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.java
new file mode 100644
index 0000000..5e8b083
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/CinemaUtilityIdentifier.java
@@ -0,0 +1,135 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+
+/**
+ * CinemaUtilityIdentifier.java
+ *
+ *
+ * Created: Thu May 25 14:27:34 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CinemaUtilityIdentifier.java,v 1.14 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CinemaUtilityIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+
+ private CinemaUtilityIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ private CinemaUtilityIdentifier( String className, String toString, boolean isInterface )
+ {
+ super( className, toString, isInterface );
+ }
+
+ public static final CinemaUtilityIdentifier CINEMA_REGEXP =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaRegexp",
+ "Provides regexp search facilities for Cinema" );
+ public static final CinemaUtilityIdentifier CINEMA_STATUS =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaStatusInformation",
+ "Provides the status bar information for cinema" );
+ public static final CinemaUtilityIdentifier CINEMA_MULTIPLE_CONSENSUS =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaMultipleConsensusViewer",
+ "Provides a viewer for many consensus sequences" );
+ public static final CinemaUtilityIdentifier CINEMA_INVOKER =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaInvoker",
+ "Provides Invoker queues for Cinema" );
+ public static final CinemaUtilityIdentifier CINEMA_SLAVE_VIEWER =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaSlaveViewerModule",
+ "Provides Slave viewers" );
+ public static final CinemaUtilityIdentifier CINEMA_RESIZE_ELEMENTS =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaResizeElements",
+ "Resizes the element size in convienient gui" );
+ public static final CinemaUtilityIdentifier CINEMA_MENU_BUILDER =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaMenuBuilder",
+ "Builds a menu system from a config tree" );
+ public static final CinemaUtilityIdentifier CINEMA_PERSIST =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaPersist",
+ "Provides persistance for cinema",
+ true );
+ public static final CinemaUtilityIdentifier CINEMA_FILE_PERSIST =
+ new CinemaUtilityIdentifier( "uk.ac.man.bioinf.apps.cinema.utils.CinemaFilePersist",
+ "Provides persistance to file for cinema" );
+} // CinemaUtilityIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: CinemaUtilityIdentifier.java,v $
+ * Revision 1.14 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.13 2001/03/12 16:47:25 lord
+ * Removed hack identifiers
+ *
+ * Revision 1.12 2001/02/19 17:21:36 lord
+ * Added regexp module
+ *
+ * Revision 1.11 2001/01/31 17:52:33 lord
+ * Changes due to removal of InterfaceIdentifier
+ * Added persistance identifiers
+ *
+ * Revision 1.10 2001/01/27 16:56:18 lord
+ * Added new module
+ *
+ * Revision 1.9 2001/01/26 17:11:13 lord
+ * Added Status info
+ *
+ * Revision 1.8 2000/11/08 18:23:55 lord
+ * Fairly uninteresting changes
+ *
+ * Revision 1.7 2000/10/19 17:51:02 lord
+ * Added more identifiers
+ *
+ * Revision 1.6 2000/09/15 17:33:12 lord
+ * Removed debug console, now in shared.
+ *
+ * Revision 1.5 2000/08/01 17:19:57 lord
+ * Added Resize module
+ *
+ * Revision 1.4 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.3 2000/06/27 15:57:39 lord
+ * Added more identifiers
+ *
+ * Revision 1.2 2000/06/05 14:17:53 lord
+ * Added support for Slave viewer module
+ *
+ * Revision 1.1 2000/05/30 16:17:11 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.java b/src/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.java
new file mode 100644
index 0000000..9f5b737
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/cinema/utils/ConsensusPercentageIDColorMap.java
@@ -0,0 +1,179 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.cinema.utils; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.util.WeakHashMap;
+import uk.ac.man.bioinf.analysis.consensus.ConsensusSequence;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculatorManager;
+import uk.ac.man.bioinf.gui.color.ColorList;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * ConsensusPercentageIDColorMap.java
+ *
+ *
+ * Created: Fri Jun 23 17:57:45 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ConsensusPercentageIDColorMap.java,v 1.6 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ConsensusPercentageIDColorMap
+ implements ColorMap, SequenceListener, AlignmentListener
+{
+ private ColorList colors = ColorList.getHotToColdColorList();
+ private WeakHashMap calcMap;
+ private SequenceAlignment alignment;
+ private int[][] colorList;
+
+ public ConsensusPercentageIDColorMap( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ calcMap = new WeakHashMap();
+ alignment.addAlignmentListener( this );
+ alignment.addSequenceListener ( this );
+ recalc();
+ }
+
+ /**
+ * Recalc everything.
+ */
+ private void recalc()
+ {
+ calcMap.clear();
+
+ colorList = new int[ alignment.getNumberSequences() ][];
+
+ for( int i = 1; i < alignment.getNumberSequences() + 1; i++ ){
+ ConsensusSequence cons = ((ConsensusSequence)alignment.getSequenceAt( i ) );
+ PercentageIDCalculator calc = PercentageIDCalculatorManager.getDefaultInstance().getCalculator
+ ( cons.getConsensusCalculator().getSequenceAlignment() );
+ calcMap.put( cons, calc );
+
+ recalc( i, calc );
+ }
+ }
+
+ private void recalc( int sequenceIndex, PercentageIDCalculator calc )
+ {
+ double[] var = calc.getVariance();
+ int[] colorAtColumn = new int[ var.length ];
+
+ for( int j = 0; j < var.length; j++ ){
+ colorAtColumn[ j ] = (int)(var[ j ] * (colors.length() -1));
+ }
+
+ colorList[ sequenceIndex - 1 ] = colorAtColumn;
+ }
+
+ private void recalc( int sequenceIndex )
+ {
+ recalc
+ ( sequenceIndex,
+ (PercentageIDCalculator)calcMap.get
+ ( alignment.getSequenceAt( sequenceIndex ) ) );
+ }
+
+ private void recalc( GappedSequence seq )
+ {
+ recalc
+ ( alignment.getSequenceIndex( seq ),
+ (PercentageIDCalculator)calcMap.get( seq ) );
+ }
+
+ public Color getColorAt(SequenceAlignment sa, Element elem, SequenceAlignmentPoint point)
+ {
+ if( elem == null ) return null;
+ return colors.getColorAt( colorList[ point.getY() - 1 ][ point.getX() - 1 ] );
+ }
+
+ public String getName()
+ {
+ return "ConsensusPercentageIDViewer";
+ }
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ recalc( (GappedSequence)event.getSource() );
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ AlignmentEventType type = event.getType();
+
+ if( type == AlignmentEventType.INSET_CHANGE ){
+ recalc( event.getStart() );
+ }
+ else{
+ // If its an insert or delete just recalc everything. In most
+ // cases this should not actually require recalculating the
+ // variances, just the final colors so it should not be too bad
+ recalc();
+ }
+ }
+} // ConsensusPercentageIDColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: ConsensusPercentageIDColorMap.java,v $
+ * Revision 1.6 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/12/18 12:12:36 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.4 2000/11/10 15:13:30 lord
+ * Major rewrite, required because the PercentageIDCalculator has totally changed.
+ *
+ * Revision 1.3 2000/08/01 15:05:16 lord
+ * Updated due to changes in PercentageIDCalculator class
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/06/27 15:56:36 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.java b/src/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.java
new file mode 100644
index 0000000..252c255
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/commandline/CalculatePercentageID.java
@@ -0,0 +1,75 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.commandline; // Package name inserted by JPack
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator;
+
+
+/**
+ * CalculatePercentageID.java
+ *
+ *
+ * Created: Tue Jan 30 17:42:44 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CalculatePercentageID.java,v 1.1 2001/02/19 17:23:49 lord Exp $
+ */
+
+public class CalculatePercentageID
+{
+ public static void main( String[] args ) throws Throwable
+ {
+ File inputFile = new File( args[ 0 ] );
+
+ PIRProteinAlignmentParser parser = new PIRProteinAlignmentParser();
+
+ ParserExceptionHandler exp = new ParserExceptionHandler(){
+ public void handleException( ParserException e )
+ {
+ e.printStackTrace();
+ }
+ };
+
+ SequenceAlignment alignment = parser.parse
+ ( new BufferedReader( new FileReader( inputFile ) ), exp );
+
+
+ PercentageIDCalculator calc = new PercentageIDCalculator( alignment );
+
+
+ double[] variance = calc.getVariance();
+
+ System.out.println( "Variance calculation:-" );
+
+ for( int i = 0; i < variance.length; i ++ ){
+ System.out.println( i + ": " + variance[ i ] );
+ }
+ } //end main method
+} // CalculatePercentageID
+
+
+
+/*
+ * ChangeLog
+ * $Log: CalculatePercentageID.java,v $
+ * Revision 1.1 2001/02/19 17:23:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.java b/src/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.java
new file mode 100644
index 0000000..f00b454
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/commandline/CheckMotifLocationAgainstPrints.java
@@ -0,0 +1,282 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.commandline; // Package name inserted by JPack
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.ResultSet;
+import java.sql.Statement;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.FileSource;
+import uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier;
+import org.apache.regexp.RE;
+import org.apache.regexp.RECompiler;
+import uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator;
+
+
+/**
+ * CheckMotifLocationAgainstPrints.java
+ *
+ * This class moves through all the SequenceAlignments in the current
+ * directory. It then extracts the motif information from PRINTS-S,
+ * and sees whether they are still in the same position.
+ *
+ * Created: Tue Feb 6 15:21:55 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: CheckMotifLocationAgainstPrints.java,v 1.1 2001/02/19 17:23:49 lord Exp $
+ */
+
+public class CheckMotifLocationAgainstPrints
+{
+
+ private static PrintWriter log;
+ private static PrintWriter error;
+ private static PrintWriter report;
+
+
+ private static Connection conn;
+
+ private static int filesChecked, filesIgnored, alignmentsNotInPrints, sequencesChecked,
+ motifsChecked, offEndOfSequence, motifMatching, motifNotMatching,
+ motifFoundInstead, motifNotFoundAtAll, offEndOfSequenceFoundElsewhere, offEndOfSequenceNotFoundElsewhere;
+
+
+ public static void main( String[] args ) throws Throwable
+ {
+ try{
+ log = new PrintWriter
+ ( new BufferedWriter( new FileWriter( new File( "log.txt" ) ) ) );
+ error = new PrintWriter
+ ( new BufferedWriter( new FileWriter( new File( "error.txt" ) ) ) );
+ report = new PrintWriter
+ ( new BufferedWriter( new FileWriter( new File( "results.txt" ) ) ) );
+
+ File director = new File( args[ 0 ] );
+ File[] files = director.listFiles();
+
+ Class.forName( "postgresql.Driver" );
+ conn = DriverManager.getConnection
+ ( "jdbc:postgresql://methionine/prints_s", "lord", "" );
+
+ for( int i = 0; i < files.length; i++ ){
+ if( files[ i ].getName().endsWith( "seqs" ) ){
+ check( files[ i ] );
+ filesChecked++;
+ }
+ else{
+ error.println( "Ignoring " + files[ i ].getName() );
+ filesIgnored++;
+ }
+ }
+ }
+
+
+ catch( Throwable t ){
+ log.close();
+ error.close();
+ throw t;
+ }
+
+ log.close();
+ error.close();
+ printReport();
+ report.close();
+ } //end main method
+
+
+ public static void printReport()
+ {
+ report.println( "Final report" );
+ report.println( "=============" );
+
+ report.println( "Files Checked: \t\t\t\t" + filesChecked );
+ report.println( "Files Ignored: \t\t\t\t" + filesIgnored );
+ report.println( "Alignments not in prints: \t\t" + alignmentsNotInPrints );
+ report.println( "Sequences checked: \t\t\t" + sequencesChecked );
+ report.println( "Motifs checked: \t\t\t" + motifsChecked );
+ report.println( "Motifs off end of sequence: \t\t" + offEndOfSequence );
+ report.println( "Motifs off end found elsewhere: \t" + offEndOfSequenceFoundElsewhere );
+ report.println( "Motifs off end not found: \t\t" + offEndOfSequenceNotFoundElsewhere );
+ report.println( "Motifs matching: \t\t\t" + motifMatching );
+ report.println( "Motifs not matching: \t\t\t" + motifNotMatching );
+ report.println( "Motifs found elsewhere: \t\t" + motifFoundInstead );
+ report.println( "Motifs not found at all: \t\t" + motifNotFoundAtAll );
+ }
+
+ // check a sequence alignment file.
+ public static void check( File file ) throws Throwable
+ {
+ log.println( "Checking " + file );
+ SequenceAlignment alignment = openFile( file );
+
+ Statement stat = conn.createStatement();
+ ResultSet res = stat.executeQuery
+ ( "select fprint_accn from fingerprint where identifier ='"
+ + alignment.getIdentifier().getTitle() + "';" );
+
+ if( !res.next() ){
+ error.println( "Fingerprint for alignment " + alignment.getIdentifier().getTitle() + " not in prints_s " );
+ alignmentsNotInPrints++;
+ return;
+ }
+
+ String fprint_accn = res.getString( "fprint_accn" );
+
+ stat.close();
+ res.close();
+
+ for( int i = 1; i < alignment.getNumberSequences() + 1; i ++ ){
+ checkSequence( alignment.getIdentifier().getTitle(), fprint_accn, alignment.getSequenceAt( i ) );
+ sequencesChecked++;
+ }
+ }
+
+ private static RE regexp = new RE();
+ private static RECompiler comp = new RECompiler();
+
+ public static void checkSequence( String alignmentTitle, String fprint_accn, GappedSequence seq ) throws Throwable
+ {
+ log.println( " Checking " + seq.getIdentifier().getTitle() );
+
+ String title = seq.getIdentifier().getTitle();
+
+ if( title.indexOf( '[' ) != -1 ){
+ title = title.substring( 0, title.indexOf( '[' ) - 1 );
+ }
+
+
+ // translate title to seqn_id if needed
+ if( title.indexOf( '_' ) != -1 ){
+ Statement stat = conn.createStatement();
+
+ ResultSet res = stat.executeQuery
+ ( "select seqn_accn from seqn where seqn_id = '" + title + "';" );
+
+ if( res.next() ){
+ title = res.getString( "seqn_accn" );
+ }
+
+ stat.close();
+ res.close();
+ }
+
+
+ // now get the motif
+ Statement stat = conn.createStatement();
+
+ ResultSet res = stat.executeQuery
+ ( "select start_position, seqn_fragment from motif where fprint_accn = '"
+ + fprint_accn + "' and seqn_accn = '" + title + "';" );// and final = true;" );
+
+ int i = 1;
+ // get the results
+ while( res.next() ){
+ motifsChecked++;
+ log.println( " Checking motif " + i );
+ int start = res.getInt( "start_position" );
+ String dataMotif = res.getString( "seqn_fragment" );
+ int length = dataMotif.length();
+
+ if( (start + length) > seq.getLength() ){
+ error.println( "For " + alignmentTitle + " motif " + i
+ + " appears to start after the end of the sequence " + title );
+ offEndOfSequence++;
+
+ regexp.setProgram( comp.compile( dataMotif ) );
+ if( regexp.match( new SequenceCharacterIterator( seq ), 0 ) ){
+ error.println( "Found instead at " + regexp.getParenStart( 0 ) + " to " + regexp.getParenEnd( 0 ) );
+ offEndOfSequenceFoundElsewhere++;
+ }
+ else{
+ error.println( "Not found motif in sequence" );
+ offEndOfSequenceNotFoundElsewhere++;
+ }
+
+ return;
+ }
+
+ String seqMotif = Sequences.getSequenceAsString( seq.getSubSequence( start, length ) );
+
+ if( !dataMotif.equals( seqMotif ) ){
+ motifNotMatching++;
+ error.println( "For " + alignmentTitle + " motif " + i
+ + " " + seqMotif + " does not match " + dataMotif + " for seq " + title );
+
+ regexp.setProgram( comp.compile( dataMotif ) );
+ if( regexp.match( new SequenceCharacterIterator( seq ), 0 ) ){
+ error.println( "Found instead at " + regexp.getParenStart( 0 ) + " to " + regexp.getParenEnd( 0 ) );
+ motifFoundInstead++;
+ }
+ else{
+ error.println( "Not found motif in sequence" );
+ motifNotFoundAtAll++;
+ }
+ }else{
+ motifMatching++;
+ }
+ i++;
+ }
+
+ stat.close();
+ res.close();
+ }
+
+ public static SequenceAlignment openFile( File inputFile ) throws Throwable
+ {
+
+ PIRProteinAlignmentParser parser = new PIRProteinAlignmentParser();
+
+ ParserExceptionHandler exp = new ParserExceptionHandler(){
+ public void handleException( ParserException e )
+ {
+ //e.printStackTrace();
+ }
+ };
+
+ String fileName = inputFile.getName();
+ int i = fileName.lastIndexOf( '.' );
+ String fileNameNoExtension = fileName;
+ if( i > 0 && i < fileName.length() - 1 ){
+ fileNameNoExtension = fileName.substring( 0, i );
+ }
+ fileNameNoExtension = fileNameNoExtension.toUpperCase();
+
+
+ SequenceAlignment alignment = parser.parse
+ ( new SimpleIdentifier( fileNameNoExtension,new FileSource( inputFile )),
+ new BufferedReader( new FileReader( inputFile ) ), exp );
+ return alignment;
+ }
+
+} // CheckMotifLocationAgainstPrints
+
+
+
+/*
+ * ChangeLog
+ * $Log: CheckMotifLocationAgainstPrints.java,v $
+ * Revision 1.1 2001/02/19 17:23:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.java b/src/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.java
new file mode 100644
index 0000000..eb46e7a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/commandline/GappedSequenceSearch.java
@@ -0,0 +1,100 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.commandline; // Package name inserted by JPack
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import org.apache.regexp.RE;
+import uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.Sequences;
+
+
+/**
+ * SequenceSearch.java
+ *
+ * Searches through a SequenceAlignment specified on the command line for
+ * all occurrences of the given regexp.
+ *
+ * Created: Mon Feb 5 14:48:30 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: GappedSequenceSearch.java,v 1.2 2001/02/20 17:55:12 lord Exp $
+ */
+
+public class GappedSequenceSearch
+{
+
+ public static void main( String[] args ) throws Throwable
+ {
+ File inputFile = new File( args[ 0 ] );
+
+ PIRProteinAlignmentParser parser = new PIRProteinAlignmentParser();
+
+ ParserExceptionHandler exp = new ParserExceptionHandler(){
+ public void handleException( ParserException e )
+ {
+ //e.printStackTrace();
+ }
+ };
+
+ SequenceAlignment alignment = parser.parse
+ ( new BufferedReader( new FileReader( inputFile ) ), exp );
+
+ Sequences.printSequence( alignment.getSequenceAt( 1 ) );
+
+ RE regexp = new RE( args[ 1 ] );
+
+ for( int i = 1; i < (alignment.getNumberSequences() + 1); i++ ){
+ scanSequence( alignment.getSequenceAt( i ), regexp );
+ }
+ } //end main method
+
+ private static void scanSequence( GappedSequence seq, RE regexp )
+ {
+ GappedSequenceCharacterIterator iter = new GappedSequenceCharacterIterator( seq );
+
+ int index = 0;
+
+ while( regexp.match( iter, index ) ){
+ System.out.println();
+ System.out.println( "Seq: " + seq.getIdentifier().getTitle()
+ + " matches at " + regexp.getParenStart( 0 ) + " to "
+ + regexp.getParenEnd( 0 ) + " with " +
+ iter.substring
+ ( regexp.getParenStart( 0 ),
+ (regexp.getParenEnd( 0 ) -
+ regexp.getParenStart( 0 ) ) ) );
+ index = regexp.getParenEnd( 0 );
+ }
+
+ if( index == 0 ) System.out.println( "Seq: " + seq.getIdentifier().getTitle() + " does not match" );
+ }
+} // SequenceSearch
+
+
+
+/*
+ * ChangeLog
+ * $Log: GappedSequenceSearch.java,v $
+ * Revision 1.2 2001/02/20 17:55:12 lord
+ * Removed extraneous import
+ *
+ * Revision 1.1 2001/02/19 17:23:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/commandline/SequenceSearch.java b/src/uk/ac/man/bioinf/apps/commandline/SequenceSearch.java
new file mode 100644
index 0000000..2196573
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/commandline/SequenceSearch.java
@@ -0,0 +1,102 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.commandline; // Package name inserted by JPack
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import org.apache.regexp.RE;
+import uk.ac.man.bioinf.analysis.regexp.GappedSequenceCharacterIterator;
+import uk.ac.man.bioinf.io.ParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.analysis.regexp.SequenceCharacterIterator;
+
+
+/**
+ * SequenceSearch.java
+ *
+ * Searches through a SequenceAlignment specified on the command line for
+ * all occurrences of the given regexp.
+ *
+ * Created: Mon Feb 5 14:48:30 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceSearch.java,v 1.2 2001/02/20 17:53:15 lord Exp $
+ */
+
+public class SequenceSearch
+{
+
+ public static void main( String[] args ) throws Throwable
+ {
+ File inputFile = new File( args[ 0 ] );
+
+ PIRProteinAlignmentParser parser = new PIRProteinAlignmentParser();
+
+ ParserExceptionHandler exp = new ParserExceptionHandler(){
+ public void handleException( ParserException e )
+ {
+ //e.printStackTrace();
+ }
+ };
+
+ SequenceAlignment alignment = parser.parse
+ ( new BufferedReader( new FileReader( inputFile ) ), exp );
+
+ Sequences.printSequence( alignment.getSequenceAt( 1 ) );
+
+ RE regexp = new RE( args[ 1 ] );
+
+ for( int i = 1; i < (alignment.getNumberSequences() + 1); i++ ){
+ scanSequence( alignment.getSequenceAt( i ), regexp );
+ }
+ } //end main method
+
+ private static void scanSequence( GappedSequence seq, RE regexp )
+ {
+ SequenceCharacterIterator iter = new SequenceCharacterIterator( seq );
+
+ int index = 0;
+
+ while( regexp.match( iter, index ) ){
+ System.out.println();
+ System.out.println( "Seq: " + seq.getIdentifier().getTitle()
+ + " matches at " + regexp.getParenStart( 0 ) + " to "
+ + regexp.getParenEnd( 0 ) + " with " +
+ iter.substring
+ ( regexp.getParenStart( 0 ),
+ (regexp.getParenEnd( 0 ) -
+ regexp.getParenStart( 0 ) ) ) );
+
+ index = regexp.getParenEnd( 0 );
+ }
+
+ if( index == 0 ) System.out.println( "Seq: " + seq.getIdentifier().getTitle() + " does not match" );
+ }
+} // SequenceSearch
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceSearch.java,v $
+ * Revision 1.2 2001/02/20 17:53:15 lord
+ * Removed extraneous import
+ *
+ * Revision 1.1 2001/02/19 17:23:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/invoker/AnonInvoker.java b/src/uk/ac/man/bioinf/apps/invoker/AnonInvoker.java
new file mode 100644
index 0000000..9a7cedf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/invoker/AnonInvoker.java
@@ -0,0 +1,105 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.invoker; // Package name inserted by JPack
+
+
+/**
+ * AnonInvoker.java
+ *
+ * This class is used with the InvokerInternalQueue. It is meant to be
+ * used as a Anonymous class hence the name. The idea is that you over
+ * ride the slow method with the program logic which takes a long
+ * time, and is done in the Queue's thread. The doRun() method on the
+ * other hand is run in the Systems main EventThread.
+ *
+ * Parameters can be passed between the slow and fast method by the
+ * "getSlowReturn" method. It is also possible to pass in a param
+ * Object when OuterClass references are not appropriate.
+ *
+ * <P>
+ * Created: Mon Dec 07 13:43:59 1998
+ * <P>
+ * Compliant: 1.1
+ * @author Phillip Lord
+ * @version $Id: AnonInvoker.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class AnonInvoker extends Invoker
+{
+ private Object slowReturn;
+
+ public AnonInvoker()
+ {
+ super( null );
+ }
+
+ public AnonInvoker( Object source )
+ {
+ super( source, null );
+ }
+
+ public AnonInvoker( Object source, Object param )
+ {
+ super( source, param );
+ }
+
+ public abstract Object slow();
+
+ public void slowImpl()
+ {
+ slowReturn = slow();
+ }
+
+ public Object getSlowReturn()
+ {
+ return slowReturn;
+ }
+} // AnonInvoker
+
+
+
+
+
+
+/*
+ * ChangeLog
+ * $Log: AnonInvoker.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/05/15 16:23:35 lord
+ * Moved pointless import
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.1 1999-02-02 16:04:10+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/invoker/Invoker.java b/src/uk/ac/man/bioinf/apps/invoker/Invoker.java
new file mode 100644
index 0000000..702c059
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/invoker/Invoker.java
@@ -0,0 +1,174 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.invoker; // Package name inserted by JPack
+import uk.ac.man.bioinf.util.ExceptionHandler;
+
+
+/**
+ * Invoker.java
+ *
+ * This class another attempt at making the sytem event queue easier
+ * in Swing. This class is meant to be used an a base implementation of
+ * runnable with a few alternative constructors, and utility methods. Its
+ * meant to be extended probably as an anonymous class to actually provide
+ * any degree of functionality.
+ *
+ * This class was originally called the "SlowInvoker". The reasons for
+ * the "Slow" are entirely historical, and relatively inappropriate.
+ *
+ * Created: Mon Dec 07 13:17:00 1998
+ *
+ * @author Phillip Lord
+ * @version $Id: Invoker.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class Invoker implements Runnable
+{
+
+ private Object source;
+ private Object param;
+ private ExceptionHandler handle;
+
+ /**
+ * Pointless constructor provided for the hell of it. Might as well
+ * extend Runnable directly if you use this.
+ */
+ public Invoker()
+ {
+ this( null, null );
+ }
+
+ /**
+ * Less Pointless constructor.
+ * Takes a parameter which is meant to be the source on the
+ * anonymous class although you could clearly use it for
+ * whatever you choose
+ * @param source the source or whatever you choose
+ */
+ public Invoker( Object source )
+ {
+ this( source, null );
+ }
+
+ /**
+ * Even more less pointless contstructor
+ * Takes a param to be used later as a parameter
+ * for the method which will be called on what is proably
+ * going to be the source. If you want to pass more than
+ * one parameter then do it thru here as an array. Type checking
+ * checking hell!
+ * @param source the source or whatever you chose
+ * @param param the param or whatever you choose
+ */
+ public Invoker( Object source, Object param )
+ {
+ this.source = source;
+ this.param = param;
+ }
+
+ public void run()
+ {
+ try{
+ doRun();
+ }
+ catch( Throwable t ){
+ //If no exception handler has been installed then as default
+ //print the stack and rethrow the exception
+ if( handle == null ){
+ t.printStackTrace();
+ }
+ //else handle the exception with the handler!
+ handle.handleException( t );
+ }
+ }
+
+
+ public abstract void doRun();
+
+ /**
+ * Get the source
+ * @return the source object
+ */
+ public Object getSource()
+ {
+ return source;
+ }
+
+ /**
+ * Get the parameter
+ * @return the parameter object
+ */
+ public Object getParameter()
+ {
+ return param;
+ }
+
+ /**
+ * Get the parameter specified by the given
+ * index. Note this requires a cast to
+ * an array, so if this doesnt work you'll get
+ * a runtime exception
+ * @param index the index of the parameter to be returned
+ */
+ public Object getParameter( int index )
+ {
+ return ((Object[])param)[ index ];
+ }
+
+ public void setExceptionHandler( ExceptionHandler handle )
+ {
+ this.handle = handle;
+ }
+} // Invoker
+
+
+
+/*
+ * ChangeLog
+ * $Log: Invoker.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/31 17:52:54 lord
+ * Exception handler moved to utils package
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.2 1999-05-14 15:10:48+01 phillip2
+ * Updated exception handling of Invoker. This necessitated
+ * a changed of method name from run to doRun. Previously an exception
+ * thrown in the run method when invoked by SwingUtilities.invokeAndWait() was
+ * getting silently swallowed. Now it either dumps stack or is passed to a Exception
+ * Handler.
+ *
+ * Revision 1.1 1999-02-02 16:04:03+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.java b/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.java
new file mode 100644
index 0000000..b9f46a2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalEventQueueException.java
@@ -0,0 +1,70 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.invoker; // Package name inserted by JPack
+
+
+/**
+ * InvokerInternalEventQueueException.java
+ *
+ * For translating a generic exception into a runtime exception
+ *
+ * Created: Fri Oct 01 15:18:01 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: InvokerInternalEventQueueException.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class InvokerInternalEventQueueException extends RuntimeException
+{
+ private Exception e;
+ public InvokerInternalEventQueueException( Exception e )
+ {
+ super( e.getMessage() );
+ this.e = e;
+ }
+
+ public Exception getException()
+ {
+ return e;
+ }
+} // InvokerInternalEventQueueException
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvokerInternalEventQueueException.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.java b/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.java
new file mode 100644
index 0000000..05ee73d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueue.java
@@ -0,0 +1,315 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.invoker; // Package name inserted by JPack
+
+import java.lang.reflect.InvocationTargetException;
+import java.util.Collections;
+import java.util.LinkedList;
+import java.util.List;
+import javax.swing.SwingUtilities;
+import uk.ac.man.bioinf.apps.systemevents.SystemEvent;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventOption;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventProducer;
+import uk.ac.man.bioinf.apps.systemevents.SystemListener;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.util.ExceptionHandler;
+
+
+
+/**
+ * InvokerInternalQueue.java
+ *
+ * This class is used as a helper mechanism for interacting with swing
+ * objects. The idea here is that you it you can place an object on
+ * this queue, and have a slow method invoked on it in a thread, and
+ * then a fast method in the system event queue, without having to
+ * worry about the threads themselves.
+ *
+ * This class originally was originally called SlowInternalQueue but
+ * Ive changed it because this was only due to historical reasons
+ * anyway.
+ *
+ * As this class contains an internal thread, with a reference to it,
+ * it will not garbage collect by itself. It contains a "destroy()"
+ * method which allows graceful shutdown. Once this method has been
+ * called on an object any attempt to enqueue to the object will throw
+ * an exception.
+ *
+ * <P>
+ * Created: Mon Dec 07 13:52:32 1998
+ * <P>
+ * Compliant:
+ * @author Phillip Lord
+ * @version
+ */
+public class InvokerInternalQueue implements Runnable, SystemListener
+{
+ private List queue;
+ private Thread internalThread;
+ private boolean oneAtATime = true;
+ //After all the vetoable possibilities have gone
+ private int systemPriority = 10;
+ //The default exception handler for this queue. This over rides
+ //any handlers set for the AnonInvoker.
+ private ExceptionHandler handle;
+ private boolean destroyed = false;
+ private SystemEventProducer producer;
+
+ public InvokerInternalQueue( )
+ {
+ this( new SystemEventProducer(){
+ public void addSystemEventListener( SystemListener listener )
+ {
+ }
+ public void removeSystemEventListener( SystemListener listener )
+ {
+ }
+ });
+ }
+
+ public InvokerInternalQueue( SystemEventProducer producer )
+ {
+ this( producer,
+ Collections.synchronizedList( new LinkedList() ) );
+ }
+
+ /**
+ * A new queue. This queue will listen for SystemClosing events and
+ * will shut down its own thread when it hears this. The list
+ * parameter needs to be a list which is mutable. This class does
+ * NOT provide any synchronisation for the list, so it needs to be
+ * synchronised appropriately. It practice this means it should be
+ * fully synchronised!
+ * @param producer
+ * @param queue
+ */
+ public InvokerInternalQueue( SystemEventProducer producer, List queue )
+ {
+ this.queue = queue;
+ this.producer = producer;
+ internalThread = new Thread( this );
+ internalThread.setPriority( Thread.MAX_PRIORITY );
+ internalThread.start();
+ producer.addSystemEventListener( this );
+ }
+
+ private boolean cont = true;
+
+ public void run()
+ {
+ while( cont ){
+ try
+ {
+ //Wait here if qu is empty
+ while( queue.isEmpty() ){
+ waitImpl();
+ }
+ //Otherwise get the next event
+ AnonInvoker event = (AnonInvoker)queue.remove( 0 );
+
+ //And invoke the slow method (via this slowImpl method
+ //which allows parameter passing.
+ event.slowImpl();
+ //Now invoke the fast method. SlowAnonInvoker already
+ //implement runnable
+
+ if ( oneAtATime ){
+ SwingUtilities.invokeAndWait( event );
+ }
+ else{
+ SwingUtilities.invokeLater( event );
+ }
+ }
+ catch( IndexOutOfBoundsException e )
+ {
+ //Doesnt matter here, will just wait till next time around
+ Debug.throwable( this, e );
+ }
+ catch( InvocationTargetException e )
+ {
+ Debug.both( this, "Have an exception in the slow internal event queue. Rethrowing it"
+ , e );
+ throw new InvokerInternalEventQueueException( e );
+ }
+ catch( InterruptedException e )
+ {
+ //If this interrupt has been signalled by the systemclosing event
+ //then close down, otherwise ignore
+ if ( systemClosing ){
+ cont = false;
+ }
+ }
+ catch( RuntimeException e ){
+ e.printStackTrace();
+ }
+ }
+ }
+
+ private synchronized void waitImpl() throws InterruptedException
+ {
+ //Will be called on the internalThread thread...
+ wait();
+ }
+
+ private synchronized void notifyImpl()
+ {
+ notifyAll();
+ }
+
+ public void makeEmpty()
+ {
+ if( destroyed ) throw new InvokerInternalQueueException( "Invoker queue has been destroyed and should not be used" );
+ //Not sure whether this is wise or not. It should
+ //stop the run() method where it lies
+ internalThread.interrupt();
+ queue.clear();
+ }
+
+ private synchronized void shutdown()
+ {
+ destroyed = true;
+ systemClosing = true;
+ internalThread.interrupt();
+ queue.clear();
+
+ // The thread will stop itself in the run method if it can. This
+ // just makes doubly sure that it does.
+ if( internalThread.isAlive() ) cont = false;
+ internalThread = null;
+ }
+
+ public boolean isDestroyed()
+ {
+ return destroyed;
+ }
+
+ /**
+ * Gracefully close down the thread
+ */
+ public synchronized void destroy()
+ {
+ shutdown();
+ producer.removeSystemEventListener( this );
+ }
+
+ public void enqueue( AnonInvoker event )
+ {
+ if( destroyed ) throw new InvokerInternalQueueException( "Invoker queue has been destroyed and should not be used" );
+ //Set the exception handler for this event.
+ if( handle != null ) event.setExceptionHandler( handle );
+ queue.add( event );
+ notifyImpl();
+ }
+
+ /**
+ * Get the value of oneAtATime.
+ * @return Value of oneAtATime.
+ */
+ public boolean getOneAtATime()
+ {
+ return oneAtATime;
+ }
+
+ /**
+ * Set the value of oneAtATime.
+ * @param oneAtATime Value to assign to oneAtATime.
+ */
+ public void setOneAtATime( boolean oneAtATime )
+ {
+ this.oneAtATime = oneAtATime;
+ }
+
+
+ public boolean systemClosing = false;
+ public synchronized void systemEventOccured( SystemEvent e )
+ {
+ if ( e.getOption() == SystemEventOption.SYSTEM_SHUTDOWN ){
+ shutdown();
+ }
+ }
+
+ public int systemListenerPriority()
+ {
+ return systemPriority;
+ }
+
+ public String toString()
+ {
+ return "InvokerInternalQueue:" + super.toString();
+ }
+} // InvokerInternalQueue
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvokerInternalQueue.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2001/01/31 17:52:54 lord
+ * Exception handler moved to utils package
+ *
+ * Revision 1.3 2000/12/05 15:06:13 lord
+ * Provided the ability to destroy objects of this class, other than
+ * by signalling a system event. Previously there was no other way to
+ * kill the internal thread. This has given rise to a new "state" for the
+ * objects of the class, namely "destroyed".
+ *
+ * Revision 1.2 2000/11/08 18:21:53 lord
+ * Added default constructor
+ * Removed references to thread.stop() which is deprecated
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.5 1999-05-14 15:14:20+01 phillip2
+ * Now installs an exception handler based on the Debug class
+ *
+ * Revision 1.4 1999-05-03 23:09:05+01 phillip2
+ * Have changed notify into notify all.
+ * Changed "if empty" to "while empty"
+ * Have removed the "suspend" and "remove" calls from makeEmpty. This is probably
+ * unnecessary. Potentially it means that some more events on the queue will run if the
+ * thread running makeEmpty is hung after the "interrupt" and before the makeEmpty
+ * call. The other problem is that its deadlock prone. It says this of these methods in the
+ * documentation. Deadlock occured with HotSpot though not the classic VM.
+ *
+ * Revision 1.3 1999-04-25 16:49:55+01 phillip2
+ * Updated due to changes in SystemListener interface
+ *
+ * Revision 1.2 1999-03-19 17:22:32+00 phillip2
+ * Removed unncessary synchronisation enqueue (the queue itself
+ * provides full sync'ing).
+ * Added toString method because threads toString is crap in 1.2
+ *
+ * Revision 1.1 1999-02-02 16:04:10+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.java b/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.java
new file mode 100644
index 0000000..ac9c95b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/invoker/InvokerInternalQueueException.java
@@ -0,0 +1,61 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.invoker; // Package name inserted by JPack
+
+
+/**
+ * InvokerInternalQueueException.java
+ *
+ *
+ * Created: Fri Dec 1 17:57:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: InvokerInternalQueueException.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class InvokerInternalQueueException extends RuntimeException
+{
+ public InvokerInternalQueueException( String message )
+ {
+ super( message );
+ }
+} // InvokerInternalQueueException
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvokerInternalQueueException.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/05 15:06:41 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.java b/src/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.java
new file mode 100644
index 0000000..0b04f83
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/invoker/InvokerThreadManager.java
@@ -0,0 +1,78 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.invoker; // Package name inserted by JPack
+import java.util.HashMap;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventProducer;
+
+
+/**
+ * InvokerThreadManager.java
+ *
+ *
+ * Created: Tue Nov 7 18:47:34 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: InvokerThreadManager.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class InvokerThreadManager
+{
+ private static InvokerInternalQueue defaultInstance = new InvokerInternalQueue();
+
+ public static InvokerInternalQueue getDefaultQueue()
+ {
+ return defaultInstance;
+ }
+
+ public static final HashMap hash = new HashMap();
+ public static InvokerInternalQueue getNamedThread( SystemEventProducer producer, String name )
+ {
+ InvokerInternalQueue qu = (InvokerInternalQueue)hash.get( name );
+
+ if( qu == null ){
+ qu = new InvokerInternalQueue( producer );
+ hash.put( name, qu );
+ }
+
+ return qu;
+ }
+} // InvokerThreadManager
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvokerThreadManager.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/08 18:22:38 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.java b/src/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.java
new file mode 100644
index 0000000..901f6a7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/FileSaveableOptions.java
@@ -0,0 +1,155 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex, and modified whilst at the
+ * University of Manchester.
+ *
+ * The initial code base is copyright by the respective
+ * employers. Modifications to the initial code base are copyright of
+ * their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the
+ * ChangeLog placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by JPack
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventProducer;
+import uk.ac.man.bioinf.util.ExceptionHandler;
+
+
+
+
+/**
+ * FileSaveableOptions.java
+ *
+ * Provides Saveable Option support with files.
+ *
+ * Created: Tue Feb 02 16:40:27 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: FileSaveableOptions.java,v 1.16 2001/05/14 17:08:18 lord Exp $
+ */
+
+public class FileSaveableOptions extends SaveableOptions
+{
+ private File configFile;
+
+ public FileSaveableOptions( File configFile, SystemEventProducer producer,
+ OptionableExceptionHandler exHandler )
+ {
+ super( producer, exHandler );
+ this.configFile = configFile;
+ loadOptions();
+ }
+
+ /**
+ * These were originally going to be abstract but you cant make
+ * abstract static methods. I guess its no big thing as thing is
+ * pretty much a one off class anyway.
+ */
+ public OutputStream getSaveStream() throws IOException
+ {
+ return new FileOutputStream( configFile );
+ }
+
+ public InputStream getLoadStream() throws IOException
+ {
+ try{
+ return new FileInputStream( configFile );
+ }
+ catch( FileNotFoundException fnfe ){
+ // convert the File not found in to the standard exception
+ // indicating that the optionable source (which might not be a
+ // file in other circumstances!) is not available.
+ throw new OptionableSourceNotFoundException( "No such file" );
+ }
+ }
+
+} // FileSaveableOptions
+
+
+
+/*
+ * ChangeLog
+ * $Log: FileSaveableOptions.java,v $
+ * Revision 1.16 2001/05/14 17:08:18 lord
+ * Added proper error handling to save and restore.
+ *
+ * Revision 1.15 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.14 2001/02/19 17:25:48 lord
+ * Small bug fix
+ *
+ * Revision 1.13 2001/01/30 15:30:15 lord
+ * This class now just provides the File support part.
+ *
+ * Revision 1.12 2001/01/30 13:59:49 lord
+ * File renamed from SaveableOptions, and repacked from the
+ * photofit directories. I have done as much as I need to get
+ * this class recompiling.
+ *
+ * Revision 1.11 1999/10/14 14:00:41 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.11 1999-10-12 15:09:44+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\options\SaveableOptions.java,v').
+ *
+ * Revision 1.10 1999-10-01 16:53:18+01 phillip2
+ * Added some imports due to changed package structure
+ *
+ * Revision 1.9 1999-09-30 15:11:05+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.9 1999-09-30 15:05:02+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\options\SaveableOptions.java,v').
+ *
+ * Revision 1.8 1999-08-04 15:56:47+01 phillip2
+ * Added more documentation
+ *
+ * Revision 1.7 1999-06-11 11:29:17+01 phillip2
+ * Removed wildcards from imports
+ * Removed reference to PhotoFitStatic
+ *
+ * Revision 1.6 1999-05-07 17:28:22+01 phillip2
+ * Changed System.out to Debug.message
+ *
+ * Revision 1.5 1999-05-06 14:05:36+01 phillip2
+ * Added some minimal exception handling
+ *
+ * Revision 1.4 1999-04-25 16:47:46+01 phillip2
+ * Updated to changed SystemListener interface
+ *
+ * Revision 1.3 1999-02-15 18:04:24+00 phillip2
+ * Removed reference to PhotoFitInstall directory which doesnt exist anymore
+ *
+ * Revision 1.2 1999-02-10 18:43:32+00 phillip2
+ * The handler now forces an update of options and sets the options
+ * handler for the optionable options during addOptionable
+ *
+ * Revision 1.1 1999-02-09 19:08:14+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.java b/src/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.java
new file mode 100644
index 0000000..234263b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/NullOptionHandler.java
@@ -0,0 +1,81 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by JPack
+
+
+/**
+ * NullOptionHandler.java
+ *
+ * An option handler object that does nothing.
+ *
+ * Created: Thu Feb 1 17:42:05 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: NullOptionHandler.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class NullOptionHandler implements OptionHandler
+{
+ private static OptionHandler instance = new NullOptionHandler();
+
+ public static OptionHandler getInstance()
+ {
+ return instance;
+ }
+
+ private NullOptionHandler()
+ {
+ }
+
+ public void addOptionable( Optionable optionable )
+ {
+ }
+
+ public void removeOptionable( Optionable optionable )
+ {
+ }
+
+ public void requestOptionUpdate( Optionable optionable )
+ {
+ }
+} // NullOptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: NullOptionHandler.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:25:48 lord
+ * Small bug fix
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/apps/optionable/OptionHandler.java b/src/uk/ac/man/bioinf/apps/optionable/OptionHandler.java
new file mode 100644
index 0000000..5cae07f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/OptionHandler.java
@@ -0,0 +1,110 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex, and modified whilst at the
+ * University of Manchester.
+ *
+ * The initial code base is copyright by the respective
+ * employers. Modifications to the initial code base are copyright of
+ * their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the
+ * ChangeLog placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by JPack
+
+
+/**
+ * OptionHandler.java
+ *
+ * Objects implementing this interface should record all of
+ * Optionable object, storing and restoring their options
+ * as necessary
+ *
+ * Created: Mon Feb 01 18:10:52 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: OptionHandler.java,v 1.7 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface OptionHandler
+{
+ /**
+ * Add an optionable object. On adding the Optionhandler
+ * should set itself as the OptionHandler for the optionable
+ * object, and call requestOptionUpdate also.
+ * @param Optionable the value to assign to Optionable
+ */
+ public void addOptionable( Optionable optionable );
+
+ /**
+ * Remove the following optionable object from
+ * the list
+ * @param optionable
+ */
+ public void removeOptionable( Optionable optionable );
+
+ /**
+ * Request that the optionable object set the the options
+ * of the optionable object via its setOptions method. This could
+ * be used for a variety of reasons, although the most obvious
+ * is a "revert to saved" option.
+ * @param optionable the optionable object
+ * @see Optionable#setOptions
+ */
+ public void requestOptionUpdate( Optionable optionable );
+
+
+} // OptionHandler
+
+
+/*
+ * ChangeLog
+ * $Log: OptionHandler.java,v $
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/01/30 14:02:49 lord
+ * Repackaged from photofit. Initial checkin.
+ *
+ * Revision 1.5 1999/10/14 14:00:40 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.5 1999-10-12 15:10:09+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\options\OptionHandler.java,v').
+ *
+ * Revision 1.4 1999-09-30 15:11:06+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.4 1999-09-30 15:04:41+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\options\OptionHandler.java,v').
+ *
+ * Revision 1.3 1999-02-10 18:56:27+00 phillip2
+ * Updated documentation of addOptionable
+ *
+ * Revision 1.2 1999-02-02 16:16:36+00 phillip2
+ * Removed getOptionable( int index) method. Theres not really any call for it.
+ *
+ * Revision 1.1 1999-02-02 16:04:12+00 phillip2
+ * Initial revision
+ *
+ */
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/optionable/Optionable.java b/src/uk/ac/man/bioinf/apps/optionable/Optionable.java
new file mode 100644
index 0000000..7a4e33d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/Optionable.java
@@ -0,0 +1,101 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex, and modified whilst at the
+ * University of Manchester.
+ *
+ * The initial code base is copyright by the respective
+ * employers. Modifications to the initial code base are copyright of
+ * their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the
+ * ChangeLog placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by JPack
+
+/**
+ * Optionable.java
+ *
+ * An object implementing this interface may be in several
+ * different states, that is provide options. These options
+ * can then be stored or in other ways treated at some
+ * time point, and may also need to be set at some point. Essentially
+ * this interface was written to provide an easy way of serialising
+ * user defined options.
+ *
+ * The options should be provided in the form of a hashtable.
+ * Every Optionable object must provide a name by which it wants
+ * to group its options, so that instances of an object do not
+ * (necessarily) conflict with each others options
+ * Created: Mon Feb 01 16:11:12 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: Optionable.java,v 1.6 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface Optionable
+{
+
+ /**
+ * This string is used as an identifier for the groups
+ * of options. It will probably be used on a per-instance
+ * basis, but could also be shared by all members of a class
+ * or by an entire application. It should probably however
+ * remain constant over time for any given Optionable object
+ * If more than one optionable object is registered with
+ * the same option handler and have the same group name the
+ * options retrieved from one object will over ride all of the
+ * others.
+ * @return the string by the group of options is known
+ */
+ public String getOptionGroupName();
+
+ /**
+ * This method provides the current state of object as a map
+ * of objects
+ * @return the options
+ */
+ public Object getOptions();
+
+ /**
+ * Sets the options for this object
+ * @param map
+ */
+ public void setOptions( Object options );
+
+
+ /**
+ * Get the value of OptionHandler.
+ * @return Value of OptionHandler.
+ */
+ public OptionHandler getOptionHandler();
+
+ /**
+ * Set the value of OptionHandler.
+ * @param OptionHandler the value to assign to OptionHandler
+ */
+ public void setOptionHandler( OptionHandler OptionHandler );
+
+} // Optionable.
+
+
+
+/*
+ * ChangeLog
+ * $Log: %
+ */
diff --git a/src/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.class b/src/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.class
new file mode 100644
index 0000000..e9d1217
Binary files /dev/null and b/src/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.class differ
diff --git a/src/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.java b/src/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.java
new file mode 100644
index 0000000..c52b884
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/OptionableExceptionHandler.java
@@ -0,0 +1,87 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by Jde-Package
+
+import java.io.IOException;
+
+/**
+ * OptionableExceptionHandler.java
+ *
+ *
+ * Created: Mon May 14 14:04:22 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: OptionableExceptionHandler.java,v 1.1 2001/05/14 17:08:18 lord Exp $
+ */
+
+public interface OptionableExceptionHandler
+{
+ /**
+ * Handle an exception occurring during the loading of options.
+ * @param exp
+ * @return true if the an attempt should be made to load the options
+ * again.
+ */
+ public boolean handleLoadException( Exception exp );
+
+ /**
+ * ClassNotFoundException can occur when reading data from the
+ * stream for a data type that does not exist. It won't normally
+ * occur.
+ * @param exp
+ * @return a <code>boolean</code> value
+ */
+ public boolean handleLoadException( ClassNotFoundException exp );
+
+ /**
+ * Signalled if some unknown IOException occurs
+ * @param iop
+ * @return a <code>boolean</code> value
+ */
+ public boolean handleLoadException( IOException iop );
+
+ /**
+ * If the optionable load file can not be found this error is signalled.
+ * @param osnfe
+ * @return a <code>boolean</code> value
+ */
+ public boolean handleLoadException( OptionableSourceNotFoundException osnfe );
+
+ /**
+ * If something nasty occurs whilst gather the optionable
+ * information occurs this is error is signalled.
+ * @param exp
+ * @return a <code>boolean</code> value
+ */
+ public boolean handleSaveException( Exception exp );
+
+ /**
+ * If the save encounters IO problems!
+ * @param io
+ * @return a <code>boolean</code> value
+ */
+ public boolean handleSaveException( IOException io );
+} // OptionableExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: OptionableExceptionHandler.java,v $
+ * Revision 1.1 2001/05/14 17:08:18 lord
+ * Added proper error handling to save and restore.
+ *
+ */
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.class b/src/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.class
new file mode 100644
index 0000000..d8393e9
Binary files /dev/null and b/src/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.class differ
diff --git a/src/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.java b/src/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.java
new file mode 100644
index 0000000..541ce24
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/OptionableSourceNotFoundException.java
@@ -0,0 +1,48 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by Jde-Package
+
+import java.io.IOException;
+/**
+ * OptionableSourceNotFoundException.java
+ *
+ *
+ * Created: Mon May 14 14:13:40 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: OptionableSourceNotFoundException.java,v 1.1 2001/05/14 17:08:18 lord Exp $
+ */
+
+public class OptionableSourceNotFoundException extends IOException
+{
+
+ public OptionableSourceNotFoundException()
+ {
+ super();
+ }
+
+ public OptionableSourceNotFoundException( String message )
+ {
+ super( message );
+ }
+} // OptionableSourceNotFoundException
+
+
+
+/*
+ * ChangeLog
+ * $Log: OptionableSourceNotFoundException.java,v $
+ * Revision 1.1 2001/05/14 17:08:18 lord
+ * Added proper error handling to save and restore.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/optionable/OptionableStateException.java b/src/uk/ac/man/bioinf/apps/optionable/OptionableStateException.java
new file mode 100644
index 0000000..2bed780
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/OptionableStateException.java
@@ -0,0 +1,66 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by JPack
+
+
+/**
+ * OptionableStateException.java
+ *
+ * This exception is thrown when an Optionable object is in an illegal
+ * state. This normally indicates that an attempt to set the
+ * Optionable state of an object that has already been set.
+ *
+ * Created: Thu Feb 1 20:39:43 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: OptionableStateException.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class OptionableStateException extends Exception
+{
+
+ public OptionableStateException( String message )
+ {
+ super( message );
+ }
+
+} // OptionableStateException
+
+
+
+/*
+ * ChangeLog
+ * $Log: OptionableStateException.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:25:48 lord
+ * Small bug fix
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/optionable/SaveableOptions.java b/src/uk/ac/man/bioinf/apps/optionable/SaveableOptions.java
new file mode 100644
index 0000000..acb76e2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/optionable/SaveableOptions.java
@@ -0,0 +1,275 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex, and modified whilst at the
+ * University of Manchester.
+ *
+ * The initial code base is copyright by the respective
+ * employers. Modifications to the initial code base are copyright of
+ * their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the
+ * ChangeLog placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.optionable; // Package name inserted by JPack
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.ObjectInput;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutput;
+import java.io.ObjectOutputStream;
+import java.io.OutputStream;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+import uk.ac.man.bioinf.apps.systemevents.SystemEvent;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventOption;
+import uk.ac.man.bioinf.apps.systemevents.SystemEventProducer;
+import uk.ac.man.bioinf.apps.systemevents.SystemListener;
+import uk.ac.man.bioinf.debug.Debug;
+
+
+
+/**
+ * SaveableOptions.java
+ *
+ * This class is used to initilise and save all of the necessary
+ * options required. This class is fully synchronized
+ * Created: Tue Feb 02 16:40:27 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: SaveableOptions.java,v 1.16 2001/05/14 17:08:18 lord Exp $
+ */
+
+public abstract class SaveableOptions implements SystemListener, OptionHandler
+{
+
+ /**
+ * We store the options in this hashtable which contains
+ * a mapping between the option group name, and the object
+ * which represents the options.
+ */
+ private Hashtable options = new Hashtable();
+ /**
+ * This stores the optionable objects which will be allocated
+ * and change from one run time to the next.
+ */
+ private Vector optionObjects = new Vector();
+
+ private OptionableExceptionHandler exHandler;
+
+ public SaveableOptions( SystemEventProducer producer,
+ OptionableExceptionHandler exHandler )
+ {
+ this.exHandler = exHandler;
+ producer.addSystemEventListener( this );
+ }
+
+ protected OptionableExceptionHandler getExceptionHandler()
+ {
+ return exHandler;
+ }
+
+ //Interface methods. SystemListener
+ public void systemEventOccured( SystemEvent event )
+ {
+ if ( event.getOption() == SystemEventOption.SYSTEM_SHUTDOWN ){
+ //Get the current state of all the optionable objects
+ synchronized( FileSaveableOptions.class ){
+ //We want to get the options of only those objects which have been created
+ //this runtime. Those which havent been created this time (because they
+ //use has acted in a way to force its loading) clearly cant have changed
+ //either so we can ignore them.
+ Enumeration enum = optionObjects.elements();
+ while( enum.hasMoreElements() ){
+ Optionable opt = (Optionable)enum.nextElement();
+ if( opt.getOptionGroupName() == null )
+ throw new RuntimeException( "The group name of an optionable option should not be null" );
+ //Now update the options held in the hashtable
+ //about this class
+ if( opt.getOptions() != null ){
+ options.put( opt.getOptionGroupName(), opt.getOptions() );
+ }
+ }
+ saveOptions();
+ }
+ }
+ }
+
+ public int systemListenerPriority()
+ {
+ //A vetoable shut down so that we can report a failure to write to
+ //file and inform the user of this event. But after the usable vetoable
+ //options
+ return 0;
+ }
+
+
+ public abstract OutputStream getSaveStream() throws IOException;
+
+ public abstract InputStream getLoadStream() throws IOException;
+
+ private void saveOptions()
+ {
+ try{
+ ObjectOutput out = new ObjectOutputStream( getSaveStream() );
+ out.writeObject( options );
+ }
+ catch( IOException io ){
+ if( exHandler.handleSaveException( io ) ){
+ saveOptions();
+ }
+ }
+ catch( Exception exp ){
+ if( exHandler.handleSaveException( exp ) ){
+ saveOptions();
+ }
+ }
+ }
+
+ protected void loadOptions()
+ {
+ try{
+ if( getLoadStream() != null ){
+ ObjectInput in = new ObjectInputStream( getLoadStream() );
+ options = (Hashtable)in.readObject();
+ }
+ else{
+ options = new Hashtable();
+ }
+ }
+ catch( ClassNotFoundException cnfe ){
+ if( exHandler.handleLoadException( cnfe ) ){
+ loadOptions();
+ }
+ }
+ catch( OptionableSourceNotFoundException osnfe ){
+ if( exHandler.handleLoadException( osnfe ) ){
+ loadOptions();
+ }
+ }
+ catch( IOException io ){
+ if( exHandler.handleLoadException( io ) ){
+ loadOptions();
+ }
+ }
+ catch( Exception exp ){
+ //Caused by there being no config file, ie this is the first run
+ if ( exHandler.handleLoadException( exp ) ){
+ loadOptions();
+ }
+ }
+ }
+
+ //OptionHandler
+ public synchronized void addOptionable( Optionable optionable )
+ {
+ if( Debug.debug ){
+ Debug.message( this, "Registering optionable object " + optionable + " with SavableOptions" );
+ }
+ //Add the optionable object to vector
+ optionObjects.add( optionable );
+ //Set the optionables optionHandler to this
+ optionable.setOptionHandler( this );
+ //Force an option update
+ requestOptionUpdate( optionable );
+ }
+
+ public synchronized void removeOptionable( Optionable optionable )
+ {
+ optionObjects.remove( optionable );
+ }
+
+ public synchronized void requestOptionUpdate( Optionable optionable )
+ {
+ //Set the options of the optionable object, by removing
+ //the options from the stored hashtable.
+ optionable.setOptions( options.get( optionable.getOptionGroupName() ) );
+ }
+
+} // SaveableOptions
+
+
+
+/*
+ * ChangeLog
+ * $Log: SaveableOptions.java,v $
+ * Revision 1.16 2001/05/14 17:08:18 lord
+ * Added proper error handling to save and restore.
+ *
+ * Revision 1.15 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.14 2001/02/19 17:25:48 lord
+ * Small bug fix
+ *
+ * Revision 1.13 2001/01/30 15:29:43 lord
+ * Resurrected this class again when I realised that it would be useful
+ * after all.
+ *
+ * Revision 1.12 2001/01/30 13:59:49 lord
+ * File renamed from SaveableOptions, and repacked from the
+ * photofit directories. I have done as much as I need to get
+ * this class recompiling.
+ *
+ * Revision 1.11 1999/10/14 14:00:41 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.11 1999-10-12 15:09:44+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\options\SaveableOptions.java,v').
+ *
+ * Revision 1.10 1999-10-01 16:53:18+01 phillip2
+ * Added some imports due to changed package structure
+ *
+ * Revision 1.9 1999-09-30 15:11:05+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.9 1999-09-30 15:05:02+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\options\SaveableOptions.java,v').
+ *
+ * Revision 1.8 1999-08-04 15:56:47+01 phillip2
+ * Added more documentation
+ *
+ * Revision 1.7 1999-06-11 11:29:17+01 phillip2
+ * Removed wildcards from imports
+ * Removed reference to PhotoFitStatic
+ *
+ * Revision 1.6 1999-05-07 17:28:22+01 phillip2
+ * Changed System.out to Debug.message
+ *
+ * Revision 1.5 1999-05-06 14:05:36+01 phillip2
+ * Added some minimal exception handling
+ *
+ * Revision 1.4 1999-04-25 16:47:46+01 phillip2
+ * Updated to changed SystemListener interface
+ *
+ * Revision 1.3 1999-02-15 18:04:24+00 phillip2
+ * Removed reference to PhotoFitInstall directory which doesnt exist anymore
+ *
+ * Revision 1.2 1999-02-10 18:43:32+00 phillip2
+ * The handler now forces an update of options and sets the options
+ * handler for the optionable options during addOptionable
+ *
+ * Revision 1.1 1999-02-09 19:08:14+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/systemevents/SystemEvent.java b/src/uk/ac/man/bioinf/apps/systemevents/SystemEvent.java
new file mode 100644
index 0000000..a65d538
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/systemevents/SystemEvent.java
@@ -0,0 +1,88 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.systemevents; // Package name inserted by JPack
+
+import java.util.EventObject;
+
+/**
+ * SystemEvent.java
+ *
+ *
+ * <P>
+ * Created: Thu Jan 14 17:51:04 1999
+ * <P>
+ * Compliant:
+ * @author Phillip Lord
+ * @version
+ */
+
+public class SystemEvent extends EventObject
+{
+ private SystemEventOption option;
+
+ public SystemEvent( Object source, SystemEventOption option )
+ {
+ super( source );
+ this.option = option;
+ }
+
+ public SystemEventOption getOption()
+ {
+ return option;
+ }
+
+} // SystemEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: SystemEvent.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.3 1999/10/14 14:01:01 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.3 1999-10-12 14:38:01+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemEvent.java,v').
+ *
+ * Revision 1.2 1999-09-30 15:01:42+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.2 1999-09-30 14:57:37+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemEvent.java,v').
+ *
+ * Revision 1.1 1999-02-02 16:04:04+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.java b/src/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.java
new file mode 100644
index 0000000..57fb9e0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/systemevents/SystemEventOption.java
@@ -0,0 +1,89 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.systemevents; // Package name inserted by JPack
+
+
+/**
+ * SystemEventOption.java
+ *
+ *
+ * <P>
+ * Created: Thu Jan 14 17:54:34 1999
+ * <P>
+ * Compliant:
+ * @author Phillip Lord
+ * @version
+ */
+
+public class SystemEventOption
+{
+ private String toString;
+
+ private SystemEventOption( String toString )
+ {
+ this.toString = toString;
+ }
+
+ public String toString()
+ {
+ return toString;
+ }
+
+ public static SystemEventOption SYSTEM_SHUTDOWN = new SystemEventOption
+ ( "System Shutting Down Event" );
+
+} // SystemEventOption.java
+
+
+
+/*
+ * ChangeLog
+ * $Log: SystemEventOption.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.3 1999/10/14 14:01:01 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.3 1999-10-12 14:37:50+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemEventOption.java,v').
+ *
+ * Revision 1.2 1999-09-30 15:01:42+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.2 1999-09-30 14:58:07+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemEventOption.java,v').
+ *
+ * Revision 1.1 1999-02-02 16:04:05+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.java b/src/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.java
new file mode 100644
index 0000000..dcd7251
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/systemevents/SystemEventProducer.java
@@ -0,0 +1,65 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.systemevents; // Package name inserted by JPack
+
+
+/**
+ * SystemEventProducer.java
+ *
+ * Interface defining the SystemEventProducer
+ *
+ * Created: Fri Oct 01 14:55:42 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: SystemEventProducer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface SystemEventProducer
+{
+ public void addSystemEventListener( SystemListener listener );
+
+ public void removeSystemEventListener( SystemListener listener );
+
+} // SystemEventProducer
+
+
+
+/*
+ * ChangeLog
+ * $Log: SystemEventProducer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.1 1999/10/21 11:31:38 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.java b/src/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.java
new file mode 100644
index 0000000..1bcd0a8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/systemevents/SystemEventSupport.java
@@ -0,0 +1,172 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+
+package uk.ac.man.bioinf.apps.systemevents; // Package name inserted by JPack
+
+import java.util.*;
+
+/**
+ * SystemEventSupport.java
+ *
+ * Provides a basic queue for holding all the listeners. Im using
+ * a priority queue here.
+ *
+ * Created: Thu Apr 15 17:44:57 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: SystemEventSupport.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class SystemEventSupport implements SystemEventProducer
+{
+ /**
+ * Internal storage
+ */
+ private ArrayList list = new ArrayList();
+ /**
+ * The value of the last listener retrieved from the
+ * list.
+ */
+ private int lastCalledPriority = Integer.MIN_VALUE;
+
+ public void addSystemEventListener( SystemListener listener )
+ {
+ list.add( new ListenerToComparable( listener ) );
+ }
+
+ public void removeSystemEventListener( SystemListener listener )
+ {
+ list.remove( new ListenerToComparable( listener ) );
+ }
+
+ public void fireSystemEvent( SystemEventOption option ) throws SystemVetoException
+ {
+ lastCalledPriority = Integer.MIN_VALUE;
+ //Sort the array list that we have into priority order
+ Collections.sort( list );
+ Iterator iter = list.iterator();
+
+ while( iter.hasNext() ){
+ SystemListener listener = ((ListenerToComparable)iter.next()).getSystemListener();
+ lastCalledPriority = listener.systemListenerPriority();
+ listener.systemEventOccured( new SystemEvent( this, option ) );
+ }
+ }
+
+ /**
+ * The priority of the last listener which this class attempted to
+ * inform of a system event. If the runSystemEvent throws an exception
+ * this method will therefore be the priority of the listener throwing
+ * that exception
+ */
+ public int getLastPriorityRun()
+ {
+ return lastCalledPriority;
+ }
+
+ private class ListenerToComparable implements Comparable
+ {
+ private SystemListener listener;
+
+ public ListenerToComparable( SystemListener listener )
+ {
+ this.listener = listener;
+ }
+
+ public int compareTo( Object rhs )
+ {
+ //Start with a cast!
+ ListenerToComparable rhsListener = (ListenerToComparable)rhs;
+ return listener.systemListenerPriority() < rhsListener.systemListenerPriority() ? - 1:
+ listener.systemListenerPriority() == rhsListener.systemListenerPriority() ? 0 : 1;
+ }
+
+ public int systemListenerPriority()
+ {
+ return listener.systemListenerPriority();
+ }
+
+ public SystemListener getSystemListener()
+ {
+ return listener;
+ }
+
+ public boolean equals( Object obj )
+ {
+ if( obj instanceof ListenerToComparable ){
+ return this.listener.equals( ((ListenerToComparable)obj).listener );
+ }
+ return false;
+ }
+
+ public int hashCode()
+ {
+ return listener.hashCode();
+ }
+ }
+} // SystemEventSupport
+
+
+
+/*
+ * ChangeLog
+ * $Log: SystemEventSupport.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 14:56:44 lord
+ * Fixed nasty bug. The inner class which wrapped the listener had not
+ * had its equals method defined properly, thereby making it impossible
+ * to remove a listener.
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.5 1999/10/14 14:01:01 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.5 1999-10-12 14:38:12+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemEventSupport.java,v').
+ *
+ * Revision 1.4 1999-10-01 16:38:22+01 phillip2
+ * now implements SystemEventProducer, new interface
+ *
+ * Revision 1.3 1999-09-30 15:01:42+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.3 1999-09-30 14:58:20+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemEventSupport.java,v').
+ *
+ * Revision 1.2 1999-05-06 14:05:13+01 phillip2
+ * Removed debug statements
+ *
+ * Revision 1.1 1999-04-20 19:18:02+01 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/systemevents/SystemListener.java b/src/uk/ac/man/bioinf/apps/systemevents/SystemListener.java
new file mode 100644
index 0000000..2305795
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/systemevents/SystemListener.java
@@ -0,0 +1,132 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.systemevents; // Package name inserted by JPack
+
+import java.util.EventListener;
+
+/**
+ * SystemListener.java
+ *
+ * Listeners to system events. At the moment this consists of ShutDown events
+ *
+ * <P>
+ * Created: Thu Jan 14 17:48:54 1999
+ * <P>
+ * Compliant:
+ * @author Phillip Lord
+ * @version
+ */
+
+public interface SystemListener extends EventListener
+{
+ /**
+ * This is an event listener for system events. All listeners
+ * should be signalled before the SystemEvent occurs. They should
+ * not return from this method until they are ready for that event
+ * to occur. An exception is thrown if the listener wishes to
+ * veto this system event. g
+ * @param e the system event occuring
+ * @exception SystemVetoException if the listener does not want the event to happen
+ */
+ public void systemEventOccured( SystemEvent e ) throws SystemVetoException;
+
+ /**
+ * Some events (particularly shut downs) have to happen in a
+ * very specific order. This method provides a priority to
+ * allow this to happen. Those with the lowest priority are
+ * informed first. Any valid int value is acceptable.
+ * This interface does not provide the ability to set different priorities
+ * for different events. The same effect can be achieved by delegating the
+ * to a small class. This way a single object can register more than one
+ * listener object, and thus have different priorities for different events
+ * A listener should not change its priority. There is not guarentee when
+ * this value will be used.
+ */
+ public int systemListenerPriority();
+
+ /*
+ * A rough guide to levels. Any value can be used
+ */
+ /**
+ * This value should be used when the System shutdown can
+ * not be aborted unless there is some error in the shutdown
+ * procedure
+ */
+ public int VETO_DUE_TO_ERROR = 0;
+ /**
+ * This value should be used when the user has full control
+ * over aborting the shutdown.
+ */
+ public int VETO_DUE_TO_USER_REQUEST = -20;
+ /**
+ * This value should be used when the system is going to
+ * shutdown regardless of errors
+ */
+ public int NO_VETO = 20;
+
+
+} // SystemListener
+
+
+/*
+ * ChangeLog
+ * $Log: SystemListener.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.5 1999/10/14 14:01:02 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.5 1999-10-12 14:37:12+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemListener.java,v').
+ *
+ * Revision 1.4 1999-09-30 15:01:41+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.4 1999-09-30 14:58:28+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemListener.java,v').
+ *
+ * Revision 1.3 1999-04-25 16:48:39+01 phillip2
+ * Added a priority to this interface
+ *
+ * Revision 1.2 1999-04-15 17:23:00+01 phillip2
+ * SystemEvent Occured can now throw an exception if the listener isnt
+ * happy. The new systemListenerPriority allows control over the order in which
+ * listeners are informed of events
+ *
+ * Revision 1.1 1999-02-02 16:04:07+00 phillip2
+ * Initial revision
+ *
+ */
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.java b/src/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.java
new file mode 100644
index 0000000..e955d91
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/systemevents/SystemVetoException.java
@@ -0,0 +1,76 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software is copyright by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ */
+
+package uk.ac.man.bioinf.apps.systemevents; // Package name inserted by JPack
+
+
+/**
+ * SystemVetoException.java
+ *
+ *
+ * Created: Thu Apr 15 17:23:20 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: SystemVetoException.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class SystemVetoException extends Exception
+{
+
+ private SystemEvent event;
+ public SystemVetoException( String message, SystemEvent event )
+ {
+ super( message );
+ this.event = event;
+ }
+
+ public SystemEvent getSystemEvent()
+ {
+ return event;
+ }
+} // SystemVetoException
+
+
+
+/*
+ * ChangeLog
+ * $Log: SystemVetoException.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.3 1999/10/14 14:01:02 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.3 1999-10-12 14:37:41+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemVetoException.java,v').
+ *
+ * Revision 1.2 1999-09-30 15:01:41+01 phillip2
+ * Updated package statement
+ *
+ * Revision 1.2 1999-09-30 14:58:43+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\systemevent\SystemVetoException.java,v').
+ *
+ * Revision 1.1 1999-04-15 18:25:15+01 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/ConfigNode.java b/src/uk/ac/man/bioinf/apps/xml/ConfigNode.java
new file mode 100644
index 0000000..97ac74c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/ConfigNode.java
@@ -0,0 +1,131 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import uk.ac.man.bioinf.module.ModuleIdentifier;
+
+
+/**
+ * ConfigNode.java
+ *
+ *
+ * Created: Tue May 9 21:45:13 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ConfigNode.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ConfigNode
+{
+ private List nodes = new LinkedList();
+ private ConfigNode[] nodeCache;
+
+ private boolean isModule;
+ private String stringData;
+ private ModuleIdentifier moduleData;
+
+ public void addChildNode( ConfigNode node )
+ {
+ nodes.add( node );
+ }
+
+ public ConfigNode[] getChildNodes()
+ {
+ if( nodeCache == null || nodes.size() != nodeCache.length ){
+ nodeCache = new ConfigNode[ nodes.size() ];
+ Iterator iter = nodes.listIterator();
+ for( int i = 0; i < nodeCache.length; i++ ){
+ nodeCache[ i ] = (ConfigNode)iter.next();
+ }
+ }
+ return nodeCache;
+ }
+
+ /**
+ * Set the data for this config node.
+ * This data is of the form ("MOD:"|"VAL:")data where data is the
+ * data which will be returned, and the first bit shows whether this
+ * is a module or not.
+ * (PENDING:- PL) This is really crap, and I think that there is no
+ * necessity for all this daft string matching. Need to remove it.
+ * @param data
+ */
+ public void setData( String data )
+ {
+ this.stringData = data;
+ isModule = false;
+ }
+
+ public void setData( ModuleIdentifier moduleIdentifer )
+ {
+ this.moduleData = moduleIdentifer;
+ isModule = true;
+ }
+
+ public boolean isModuleIdentifier()
+ {
+ return isModule;
+ }
+
+ public String getStringData()
+ {
+ return stringData;
+ }
+
+ public ModuleIdentifier getModuleData()
+ {
+ return moduleData;
+ }
+} // ConfigNode
+
+
+
+/*
+ * ChangeLog
+ * $Log: ConfigNode.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/05/30 16:19:17 lord
+ * Made this class a little bit more type safe.
+ * Sorted imports
+ *
+ * Revision 1.2 2000/05/18 17:08:58 lord
+ * Major replumping, and a few new methods
+ *
+ * Revision 1.1 2000/05/15 16:23:53 lord
+ * Initial checkin
+ *
+ */
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java b/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java
new file mode 100644
index 0000000..c8ae352
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/DefaultXMLParser.java
@@ -0,0 +1,119 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+import org.xml.sax.helpers.DefaultHandler;
+import org.xml.sax.helpers.XMLReaderFactory;
+import uk.ac.man.bioinf.debug.Debug;
+
+
+/**
+ * DefaultXMLParser.java
+ *
+ *
+ * Created: Mon May 8 21:08:32 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultXMLParser.java,v 1.5 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultXMLParser implements XMLParserFactory
+{
+ public XMLReader getXMLParser()
+ {
+ try{
+ XMLReader read = XMLReaderFactory.createXMLReader( "org.apache.xerces.parsers.SAXParser" );
+ read.setEntityResolver
+ ( new DefaultHandler(){
+ public InputSource resolveEntity( String publicId, String systemId ) throws SAXException
+ {
+ InputSource retn = super.resolveEntity( publicId, systemId );
+ System.out.println( "ENTITY:- " + retn + " pub " + publicId + " sys " + systemId );
+ return retn;
+ }
+ });
+ return read;
+ }
+ catch( Exception exp ){
+ if( Debug.debug )
+ Debug.throwable( this, exp );
+ }
+ return null;
+ }
+} // DefaultXMLParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultXMLParser.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/18 12:12:53 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.3 2000/10/19 17:51:15 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ * Revision 1.1 2000/05/15 16:23:53 lord
+ * Initial checkin
+ *
+ */
+
+/*
+ * ChangeLog
+ * $Log: DefaultXMLParser.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/18 12:12:53 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.3 2000/10/19 17:51:15 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ * Revision 1.1 2000/05/15 16:23:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.java b/src/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.java
new file mode 100644
index 0000000..d56a6e4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/XMLBootIdentifier.java
@@ -0,0 +1,69 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+
+
+/**
+ * XMLBootIdentifier.java
+ *
+ *
+ * Created: Thu May 25 11:57:19 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLBootIdentifier.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class XMLBootIdentifier extends AbstractEnumeratedModuleIdentifier
+{
+ private XMLBootIdentifier( String className, String toString )
+ {
+ super( className, toString );
+ }
+
+ public static final XMLBootIdentifier XML_BOOT =
+ new XMLBootIdentifier( "uk.ac.man.bioinf.apps.xml.XMLBootModule",
+ "Main Boot Module for reading XML config files" );
+} // XMLBootIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLBootIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/07/26 13:27:58 lord
+ * Changed due to a spelling mistake in the super class name
+ *
+ * Revision 1.1 2000/05/30 16:19:35 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/XMLBootModule.java b/src/uk/ac/man/bioinf/apps/xml/XMLBootModule.java
new file mode 100644
index 0000000..2aa0c1a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/XMLBootModule.java
@@ -0,0 +1,530 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.LinkedList;
+import java.util.Properties;
+import org.xml.sax.Attributes;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.XMLReader;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.module.AbstractEnumeratedModuleIdentifier;
+import uk.ac.man.bioinf.module.GenericModuleIdentifier;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleException;
+import uk.ac.man.bioinf.module.ModuleExceptionType;
+import uk.ac.man.bioinf.module.ModuleIdentifier;
+import uk.ac.man.bioinf.module.ModuleFactoryInstance;
+
+
+/**
+ * XMLBootModule.java
+ *
+ * This is a module which loads other modules by parsing an XML file
+ * defined by the module DTD. For itself it requires a single
+ * parameter which is the file to start parsing. It can also take a
+ * second parameter which defines the class to use to get the initial
+ * parser instance, which should extend and override the DefaultXMLParser class.
+ * The class has been written this way because at the
+ * moment neither the SAX or the DOM parser API actually defines how
+ * this is done and it varies from parser to parser.
+ *
+ * Once the files have been read there is really no need to hold a
+ * copy of the object structure in memory so this class uses the SAX
+ * parser. Ive decided to use SAX2, which is still in beta for several
+ * of the publically available parsers. Hopefully this wont be a problem.
+ *
+ * Created: Mon May 8 20:37:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLBootModule.java,v 1.21 2002/03/08 17:44:44 lord Exp $
+ */
+
+public abstract class XMLBootModule extends Module
+{
+ // actual logic for the module loading
+
+
+ // these store the last information to have come through. Normally
+ // this would be a pretty sloppy way of doing this, as it makes a
+ // lot of assumptions about the correctness of the event stream
+ // coming in, but in the case we can guarantee this simply enough
+ // by turning on the XML validation.
+ // This class is designed to work, not to be efficient!
+ private MiniStack pcDataStack = new MiniStack();
+ private MiniStack classStack = new MiniStack();
+ private MiniStack nameStack = new MiniStack();
+ private MiniStack identifierStack = new MiniStack();
+ private MiniStack nodeStack = new MiniStack();
+ private MiniStack treeStack = new MiniStack();
+ private MiniStack valueStack = new MiniStack();
+ private MiniStack valueLastStack = new MiniStack();
+ private MiniStack paramNameStack = new MiniStack();
+
+
+ private boolean identifierConcrete = false;
+ private boolean readRequired = true;
+ private Properties configProperties;
+ private ConfigNode configTree;
+ private Object[] configObject;
+ private String provideName;
+
+ // pc data. Stuff it onto the stack
+ public void characters( String chars )
+ {
+ pcDataStack.push( chars );
+ }
+
+ // move the class name on to the class stack
+ public void classEnd()
+ {
+ classStack.push( pcDataStack.pop() );
+ }
+
+ // move the name onto the stack
+ public void nameEnd()
+ {
+ nameStack.push( pcDataStack.pop() );
+ valueLastStack.push( Boolean.FALSE );
+ }
+
+ public void paramnameEnd()
+ {
+ paramNameStack.push( pcDataStack.pop() );
+ }
+
+ public void identifierStart( Attributes attribute )
+ {
+ if( attribute.getValue( "concrete" ) != null ){
+ identifierConcrete = attribute.getValue( "concrete" ).equals( "true" );
+ }
+ else{
+ identifierConcrete = true;
+ }
+ }
+
+ public void enumerationEnd()
+ {
+ try{
+ // load the enumeration class and get all of its identifiers
+ ModuleIdentifier[] ident = AbstractEnumeratedModuleIdentifier.getAllIdentifiers
+ ( Class.forName( (String)classStack.pop() ) );
+ // stuff them into the factory
+ getContext().getModuleFactory().addIdentifier( ident );
+ }
+ catch( ClassNotFoundException cnfe ){
+ // (PENDING:- PL) Need to do something better with this.
+ if( Debug.debug )
+ Debug.both( this, "Can not load enumerated identifiers", cnfe );
+ }
+ }
+
+ public void genericEnd()
+ {
+ ModuleIdentifier ident;
+
+ ident = new GenericModuleIdentifier
+ ( (String)classStack.pop(), (String)nameStack.pop(), !identifierConcrete );
+
+ getContext().getModuleFactory().addIdentifier( ident );
+ }
+
+ public void startEnd()
+ {
+ String name = (String)nameStack.pop();
+
+ try{
+ // the get method ensures that start has been called
+ getContext().getModuleFactory().getModule( getContext().getModuleFactory().resolveModuleName( name ) );
+ }
+ catch( ModuleException mod ){
+ // I don't really want this to be fatal....
+ mod.printStackTrace();
+ }
+ }
+
+ public void loadEnd() throws SAXException
+ {
+ try{
+ String moduleName = (String)nameStack.pop();
+ ModuleIdentifier ident = getContext().getModuleFactory().resolveModuleName( moduleName );
+ if( ident == null ) {
+ throw new ModuleException( "Could not resolve name " + moduleName,
+ ModuleExceptionType.MODULE_RESOLVE_FAIL );
+ }
+ getContext().getModuleFactory().load( ident );
+
+ }
+ catch( ModuleException me ){
+ // (PENDING:- PL) This should probably be a lot better!
+ me.printStackTrace();
+ }
+ }
+
+ public void readStart( Attributes attribute )
+ {
+ if( attribute.getValue( "required" ) != null ){
+ readRequired = attribute.getValue( "required" ).equals( "true" );
+ }
+ else{
+ readRequired = true;
+ }
+ }
+
+ public void readEnd() throws SAXException
+ {
+ String parse = (String)pcDataStack.pop();
+ parseResource( parse, readRequired );
+ }
+
+ public void valueEnd()
+ {
+ valueStack.push( pcDataStack.pop() );
+ valueLastStack.push( Boolean.TRUE );
+ }
+
+ public void paramEnd()
+ {
+ configProperties.setProperty
+ ( (String)paramNameStack.pop(),
+ (String)((((Boolean)valueLastStack.pop()).booleanValue())
+ ? ("VAL:" + valueStack.pop()) : ("MOD:" + nameStack.pop()) ) );
+ }
+
+ public void propertiesStart()
+ {
+ if( configObject[ 0 ] == null ){
+ configProperties = new Properties();
+ }
+ else{
+ configProperties = (Properties)configObject[ 0 ];
+ }
+ }
+
+ public void propertiesEnd()
+ {
+ configObject[ 0 ] = configProperties;
+ configProperties = null;
+ }
+
+ public void provideEnd()
+ {
+ provideName = (String)nameStack.pop();
+ }
+
+ public void configStart( Attributes attrib )
+ {
+ String val = attrib.getValue( "mode" );
+
+ if( val == null || val.equals( "add" ) ){
+ ModuleIdentifier ident = getContext().getModuleFactory().resolveModuleName( (String)nameStack.peek() );
+ if( ident != null ){
+ configObject = (Object[])getContext().getModuleFactory().getConfig( ident );
+ }
+ }
+
+ if( configObject == null ){
+ configObject = new Object[ 2 ];
+ }
+ }
+
+ public void moduleEnd()
+ {
+ ModuleFactoryInstance fact = getContext().getModuleFactory();
+
+ ModuleIdentifier ident = fact.resolveModuleName( (String)nameStack.pop() );
+
+ if( provideName != null ){
+ // if the provide name is not null, then this Module should in
+ // fact be delegating its functionality to elsewhere, because
+ // its an interface module. So we need to associate the module
+ // providing this implementation with the identifier.
+ fact.setConcreteIdentifier( ident, fact.resolveModuleName( provideName ) );
+ provideName = null;
+ }
+
+ getContext().getModuleFactory().setConfig( ident, configObject );
+ configObject = null;
+ }
+
+ public void treeStart()
+ {
+ if( configObject[ 1 ] == null ){
+ configTree = new ConfigNode();
+ }
+ else{
+ configTree = (ConfigNode)configObject[ 1 ];
+ }
+ }
+
+ public void nodeStart()
+ {
+ nodeStack.push( new ConfigNode() );
+ }
+
+ public void nodeEnd()
+ {
+ // get the last node
+ ConfigNode last = (ConfigNode)nodeStack.pop();
+
+ // set its value correctly.
+ if( ((Boolean)valueLastStack.pop()).booleanValue() ){
+ last.setData( (String)valueStack.pop() );
+ }
+ else{
+ last.setData( getContext().resolveModuleName( (String)nameStack.pop() ) );
+ }
+
+ // now stuff this node into the node above if it exists, or the
+ // configTree if it doesnt.
+ if( nodeStack.peek() == null ){
+ configTree.addChildNode( last );
+ }
+ else{
+ ((ConfigNode)nodeStack.peek()).addChildNode( last );
+ }
+ }
+
+ public void treeEnd()
+ {
+ configObject[ 1 ] = configTree;
+ configTree = null;
+ }
+
+ public void load() throws ModuleException
+ {
+ try{
+ parseResource( fetchMainBootName(), true );
+
+ // let all this stuff get gc'd
+ pcDataStack =
+ classStack =
+ nameStack =
+ identifierStack =
+ nodeStack =
+ treeStack =
+ valueStack =
+ valueLastStack =
+ paramNameStack = null;
+
+ configObject = null;
+ configTree = null;
+ configProperties = null;
+ }
+ catch( SAXException sax ){
+ throw new ModuleException( "Problem parsing file ", ModuleExceptionType.MODULE_INIT_PROBLEM, sax );
+ }
+ }
+
+ public void parseResource( String name, boolean required ) throws SAXException
+ {
+ try{
+ parseStream( resolveXMLLoadName( name ) );
+ }
+ catch( FileNotFoundException fnfe ){
+ // throw this if required...
+ if( required ){
+ throw new SAXException( "IO Problem with file " + name, fnfe );
+ }
+ }
+ catch( IOException io ){
+ throw new SAXException( "IO Problem with file " + name, io );
+ }
+ }
+
+ public void parseStream( InputStream stream ) throws IOException, SAXException
+ {
+ try{
+
+ XMLReader parser = getXMLParser();
+ //parser.setFeature("http://xml.org/sax/features/validation", true);
+
+ XMLBootParserListener listener = new XMLBootParserListener( this );
+
+ parser.setContentHandler( listener );
+
+ //parser.setErrorHandler( listener );
+ InputSource inp =
+ ( new InputSource( stream ) );
+ inp.setSystemId
+ ( fetchModuleSystemIdentifier() );
+
+ parser.parse( inp );
+ }
+ catch( SAXException se ){
+ if( Debug.debug ){
+ Debug.both( this, "Sax exception during parsing", se );
+ Debug.both( this, "Original Exception was", se.getException() );
+ }
+ else{
+ throw se;
+ }
+ }
+ }
+
+ public String getVersion()
+ {
+ return "$Id: XMLBootModule.java,v 1.21 2002/03/08 17:44:44 lord Exp $";
+ }
+
+ private XMLReader getXMLParser()
+ {
+ try{
+ XMLParserFactory parserGen =
+ (XMLParserFactory)Class.forName( getXMLParserClass() ).newInstance();
+ return parserGen.getXMLParser();
+ }
+ catch( Exception exp ){
+ if( Debug.debug )
+ Debug.throwable( this, exp );
+ }
+ return null;
+ }
+
+ protected String getXMLParserClass()
+ {
+ // (PENDING:- PL) This will be configurable
+ return DefaultXMLParser.class.getName();
+ }
+
+ public abstract String fetchMainBootName();
+
+ public abstract String fetchModuleSystemIdentifier();
+
+ public abstract InputStream resolveXMLLoadName( String name ) throws IOException;
+
+ // dig dem funky method names
+ public class MiniStack
+ {
+ private LinkedList list = new LinkedList();
+ public void push( Object object )
+ {
+ list.addFirst( object );
+ }
+
+ public Object peek()
+ {
+ if( list.size() == 0 ) return null;
+ return list.getFirst();
+ }
+
+ public Object pop()
+ {
+ if( list.size() == 0 ) return null;
+ return list.removeFirst();
+ }
+ }
+
+} // XMLBootModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLBootModule.java,v $
+ * Revision 1.21 2002/03/08 17:44:44 lord
+ * Switch off validation
+ *
+ * Revision 1.20 2001/05/08 15:53:06 lord
+ * Set validation to true
+ *
+ * Revision 1.19 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.18 2001/01/31 17:53:49 lord
+ * Changes due to removal of InterfaceIdentifier
+ * More exception handling update. This class is due
+ * for a complete overhaul in its exception handling.
+ *
+ * Revision 1.17 2001/01/26 17:11:46 lord
+ * Improved exception handling.
+ * Loading config from multiple places
+ *
+ * Revision 1.16 2001/01/19 19:47:45 lord
+ * Removed debug
+ *
+ * Revision 1.15 2001/01/15 18:42:56 lord
+ * Support for the read required attribute
+ * Improved the exception handling. Can not give an informative stack
+ * trace when an exception is thrown.
+ *
+ * Revision 1.14 2000/10/19 17:51:52 lord
+ * Import rationalisation.
+ * Improved error handling, so that this class does not swallow errors
+ * when Debug.debug is false.
+ *
+ * Revision 1.13 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ * Revision 1.12 2000/09/15 17:24:42 lord
+ * No longer uses the ModuleFactory.
+ *
+ * Revision 1.11 2000/08/03 16:38:24 lord
+ * Modifications to enable Cinema to run from jar file
+ *
+ * Revision 1.10 2000/08/01 17:11:41 lord
+ * Updated support for GenericModuleIdentifier
+ *
+ * Revision 1.9 2000/07/26 13:36:01 lord
+ * Modified due to name change for AbstractEnumeratedModuleIdentifier
+ *
+ * Revision 1.8 2000/07/18 11:07:44 lord
+ * Cosmetic
+ *
+ * Revision 1.7 2000/06/27 15:57:58 lord
+ * Improved documentation
+ *
+ * Revision 1.6 2000/06/05 14:19:22 lord
+ * Have neatened up the way the node tree is built. I actually
+ * understand the code that I have written now!
+ *
+ * Revision 1.5 2000/05/30 16:55:22 lord
+ * Horrible mess up in last checkin
+ *
+ * Revision 1.4 2000/05/30 16:21:55 lord
+ * Many changes. Imports. Added support for more elements.
+ * Fixed dubious mechanism for module configuration.
+ * Class now abstract to allow subclass to locate the XML files it
+ * needs. Changes due to completion of module architecture.
+ *
+ * Revision 1.3 2000/05/24 15:38:03 lord
+ * MiniStack does not need to extend LinkedList
+ *
+ * Revision 1.2 2000/05/18 17:09:21 lord
+ * Lots of new methods
+ *
+ * Revision 1.1 2000/05/15 16:23:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.java b/src/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.java
new file mode 100644
index 0000000..31b9e94
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/XMLBootParserListener.java
@@ -0,0 +1,276 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+
+import org.xml.sax.Attributes;
+import org.xml.sax.ContentHandler;
+import org.xml.sax.ErrorHandler;
+import org.xml.sax.Locator;
+import org.xml.sax.SAXException;
+import org.xml.sax.SAXParseException;
+import uk.ac.man.bioinf.debug.Debug;
+
+/**
+ * XMLBootParserListener.java
+ *
+ *
+ * Created: Tue May 9 22:10:53 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLBootParserListener.java,v 1.13 2001/05/08 17:46:50 lord Exp $
+ */
+
+public class XMLBootParserListener implements ErrorHandler, ContentHandler
+{
+ private static final boolean localDebug = false;
+ private XMLBootModule mod;
+
+ public XMLBootParserListener( XMLBootModule mod )
+ {
+ this.mod = mod;
+ }
+
+ public void setDocumentLocator( Locator locator )
+ {
+ if( Debug.debug || localDebug )
+ Debug.message( this, "XML Parse: Have recieved document locator" );
+ }
+
+ public void startDocument()
+ {
+ if( Debug.debug || localDebug )
+ Debug.message( this, "XML Parse: Starting document" );
+ }
+
+ public void endDocument()
+ {
+ if( Debug.debug || localDebug )
+ Debug.message( this, "XML Parse: Ending document" );
+ }
+
+ public void startPrefixMapping( String prefix, String uri )
+ {
+ }
+
+ public void endPrefixMapping( String prefix )
+ {
+ }
+
+ public void startElement( String nameSpaceUri, String localName, String rawName, Attributes attrib )
+ {
+ if( Debug.debug || localDebug )
+ Debug.message( this, "XML Parse: Start element. NSURI: " + nameSpaceUri + " Local: " + localName
+ + " Raw: " + rawName );
+ String elem = rawName;
+
+ if( elem.equals( "properties" ) ){
+ mod.propertiesStart();
+ }
+
+ if( elem.equals( "identifier" ) ){
+ mod.identifierStart( attrib );
+ }
+
+ if( elem.equals( "node" ) ){
+ mod.nodeStart();
+ }
+
+ if( elem.equals( "tree" ) ){
+ mod.treeStart();
+ }
+
+ if( elem.equals( "config" ) ){
+ mod.configStart( attrib );
+ }
+
+ if( elem.equals( "read" ) ){
+ mod.readStart( attrib );
+ }
+ }
+
+ public void endElement( String nameSpaceUri, String localName, String rawName ) throws SAXException
+ {
+ if( Debug.debug || localDebug )
+ Debug.message( this, "XML Parse: End element " + nameSpaceUri + " " + localName
+ + " " + rawName );
+
+ String elem = localName;
+
+ if( elem.equals( "class" ) ){
+ mod.classEnd();
+ }
+
+ if( elem.equals( "name" ) ){
+ mod.nameEnd();
+ }
+
+ if( elem.equals( "enumeration" ) ){
+ mod.enumerationEnd();
+ }
+
+ if( elem.equals( "generic" ) ){
+ mod.genericEnd();
+ }
+
+ if( elem.equals( "start" ) ){
+ mod.startEnd();
+ }
+
+ if( elem.equals( "load" ) ){
+ mod.loadEnd();
+ }
+
+ if( elem.equals( "value" ) ){
+ mod.valueEnd();
+ }
+
+ if( elem.equals( "paramname" ) ){
+ mod.paramnameEnd();
+ }
+
+ if( elem.equals( "param" ) ){
+ mod.paramEnd();
+ }
+
+ if( elem.equals( "properties" ) ){
+ mod.propertiesEnd();
+ }
+
+ if( elem.equals( "module" ) ){
+ mod.moduleEnd();
+ }
+
+ if( elem.equals( "read" ) ){
+ mod.readEnd();
+ }
+
+ if( elem.equals( "node" ) ){
+ mod.nodeEnd();
+ }
+
+ if( elem.equals( "tree" ) ){
+ mod.treeEnd();
+ }
+
+ if( elem.equals( "provide" ) ){
+ mod.provideEnd();
+ }
+ }
+
+ public void characters( char[] ch, int start, int length )
+ {
+ if( Debug.debug || localDebug ){
+ Debug.message( this, "XML Parse: Characters " + new String( ch, start, length ) );
+ }
+ mod.characters( new String( ch, start, length ) );
+ }
+
+ public void ignorableWhitespace( char[] cha, int start, int length )
+ {
+ }
+
+ public void processingInstruction( String target, String data )
+ {
+ }
+
+ public void skippedEntity( String name )
+ {
+ }
+
+ // implementation of org.xml.sax.ErrorHandler interface
+ public void error(SAXParseException param1) throws SAXException
+ {
+ if( Debug.debug || localDebug )
+ Debug.both( this, "XML Parse Error", param1 );
+ Debug.message( this, "SaxParseException at " + param1.getLineNumber() + ":" + param1.getColumnNumber() );
+ throw param1;
+ }
+
+ public void fatalError(SAXParseException param1) throws SAXException {
+ if( Debug.debug || localDebug )
+ Debug.both( this, "XML Parse Error", param1 );
+ Debug.message( this, "SaxParseException at " + param1.getLineNumber() + ":" + param1.getColumnNumber() );
+ throw param1;
+ }
+
+ public void warning(SAXParseException param1) throws SAXException {
+ if( Debug.debug || localDebug )
+ Debug.both( this, "XML Parse Error", param1 );
+ Debug.message( this, "SaxParseException at " + param1.getLineNumber() + ":" + param1.getColumnNumber() );
+ throw param1;
+ }
+} // XMLBootParserListener
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLBootParserListener.java,v $
+ * Revision 1.13 2001/05/08 17:46:50 lord
+ * Have local debug option as I seem to need this so much.
+ *
+ * Revision 1.12 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.11 2001/01/31 17:54:06 lord
+ * Sorted imports
+ *
+ * Revision 1.10 2001/01/26 17:12:05 lord
+ * config element now takes attributes
+ *
+ * Revision 1.9 2001/01/15 18:43:48 lord
+ * Improved exception handling.
+ * Support for read required attribute
+ *
+ * Revision 1.8 2000/09/15 17:24:21 lord
+ * More useful debug output
+ *
+ * Revision 1.7 2000/08/03 16:38:24 lord
+ * Modifications to enable Cinema to run from jar file
+ *
+ * Revision 1.6 2000/07/26 13:36:24 lord
+ * Bug fix. Properties start now called correctly
+ *
+ * Revision 1.5 2000/06/05 14:20:21 lord
+ * Need to catch tree start now, to allow me to neaten up the
+ * XMLBootModule code
+ *
+ * Revision 1.4 2000/05/30 16:55:22 lord
+ * Horrible mess up in last checkin
+ *
+ * Revision 1.3 2000/05/30 16:22:20 lord
+ * Support for more elements
+ *
+ * Revision 1.2 2000/05/18 17:09:38 lord
+ * Support for lots more tags
+ *
+ * Revision 1.1 2000/05/15 16:23:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/XMLModule.java b/src/uk/ac/man/bioinf/apps/xml/XMLModule.java
new file mode 100644
index 0000000..d42160b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/XMLModule.java
@@ -0,0 +1,94 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.Module;
+import java.util.Properties;
+
+
+/**
+ * XMLModule.java
+ *
+ * This class provides configuration information specific to the
+ * XMLModules. Currently there are two forms of configuration
+ * information. The first is a properties file, whilst the second is
+ * tree structure. These are independent and either or neither of
+ * these can be present.
+ *
+ * Created: Mon May 15 22:06:23 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLModule.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class XMLModule extends Module
+{
+ private boolean haveGotConfig = false;
+ private Properties props;
+ private ConfigNode rootNode;
+
+ private void breakOpenConfig()
+ {
+ Object[] configObj = (Object[])getContext().getConfig();
+
+ props = (configObj[ 0 ] != null ) ? (Properties)configObj[ 0 ] : null;
+ rootNode = (configObj[ 1 ] != null ) ? (ConfigNode)configObj[ 1 ] : null;
+ haveGotConfig = true;
+ }
+
+ public Properties getConfigProperties()
+ {
+ if( !haveGotConfig ) breakOpenConfig();
+
+ return props;
+ }
+
+ public ConfigNode getConfigTree()
+ {
+ if( !haveGotConfig ) breakOpenConfig();
+
+ return rootNode;
+ }
+
+} // XMLModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLModule.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/06/05 14:20:44 lord
+ * Now abstract, and no longer implements getVersion method
+ *
+ * Revision 1.1 2000/05/18 17:10:48 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/XMLParserFactory.java b/src/uk/ac/man/bioinf/apps/xml/XMLParserFactory.java
new file mode 100644
index 0000000..ddef65a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/XMLParserFactory.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml; // Package name inserted by JPack
+import org.xml.sax.XMLReader;
+
+
+/**
+ * XMLParserFactory.java
+ *
+ *
+ * Created: Mon Sep 18 18:52:56 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLParserFactory.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface XMLParserFactory
+{
+
+ public XMLReader getXMLParser();
+
+} // XMLParserFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLParserFactory.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/25 16:35:34 lord
+ * Changes made so that the XMLParser used is no longer hard coded
+ * but comes from a factory. This allows for instance giving the parser a
+ * custom entity resolver.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.java b/src/uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.java
new file mode 100644
index 0000000..e89c25a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/test/XMLLoadingTest.java
@@ -0,0 +1,116 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.NullModuleFactory;
+import java.util.Properties;
+import uk.ac.man.bioinf.module.ModuleIdentifier;
+import uk.ac.man.bioinf.apps.xml.ConfigNode;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.debug.NullDebug;
+
+
+/**
+ * XMLLoadingTest.java
+ *
+ *
+ * Created: Tue May 16 12:35:51 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLLoadingTest.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class XMLLoadingTest extends NullModuleFactory
+{
+
+ public void addConfig( ModuleIdentifier ident, Object config )
+ {
+ //pull open the config information
+ Object[] confAr = (Object[])config;
+ Properties props = (Properties)confAr[ 0 ];
+ ConfigNode node = (ConfigNode)confAr[ 1 ];
+
+ System.out.println( "Properties config is :-" );
+ props.list( System.out );
+
+ System.out.println( "Config nodes are:- " );
+ System.out.println( node );
+
+ printNode( node );
+ }
+
+ public static void printNode( ConfigNode node )
+ {
+ printNode( node, 0 );
+ }
+
+ public static void printNode( ConfigNode node, int step )
+ {
+ System.out.print( step + "; " + node + " " );
+ if( node.isModuleIdentifier() ){
+ System.out.println( "Mod data: " + node.getModuleData() );
+ }
+ else{
+ System.out.println( "Strng data: " + node.getStringData() );
+ }
+
+ ConfigNode[] child = node.getChildNodes();
+ for( int i = 0; i < child.length; i++ ){
+ printNode( child[ i ], step + 1 );
+ }
+ }
+
+ public static void main( String[] args )
+ {
+ // the class is now really knackered
+ Debug.setInstance( new NullDebug() );
+ //XMLBootModule mod = new XMLBootModule();
+ //mod.load();
+ } //end main method
+
+
+} // XMLLoadingTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLLoadingTest.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/06/05 14:20:57 lord
+ * Boring changes
+ *
+ * Revision 1.2 2000/05/30 16:22:33 lord
+ * Boring changes
+ *
+ * Revision 1.1 2000/05/18 17:15:18 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/apps/xml/test/XMLStartTest.java b/src/uk/ac/man/bioinf/apps/xml/test/XMLStartTest.java
new file mode 100644
index 0000000..cd569ed
--- /dev/null
+++ b/src/uk/ac/man/bioinf/apps/xml/test/XMLStartTest.java
@@ -0,0 +1,67 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.apps.xml.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.xml.XMLBootIdentifier;
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleFactoryInstance;
+
+/**
+ * XMLStartTest.java
+ *
+ *
+ * Created: Thu May 25 12:05:07 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: XMLStartTest.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class XMLStartTest
+{
+ public static void main( String[] args ) throws Throwable
+ {
+ ModuleFactoryInstance inst = new uk.ac.man.bioinf.module.DefaultModuleFactoryInstance();
+ inst.addIdentifier( XMLBootIdentifier.XML_BOOT );
+ inst.load( XMLBootIdentifier.XML_BOOT );
+ } //end main method
+
+
+} // XMLStartTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: XMLStartTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/18 11:07:57 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/bin/cinema b/src/uk/ac/man/bioinf/bin/cinema
new file mode 100644
index 0000000..85ea182
--- /dev/null
+++ b/src/uk/ac/man/bioinf/bin/cinema
@@ -0,0 +1,84 @@
+#!/bin/sh
+
+###
+### Launch script for Cinema.
+###
+### Copyright (c) 2001 Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+
+###
+### This is the definative launch script for Cinema. I have scripts in
+### other languages also, but if they differ in their functionality,
+### all the others are wrong and this one is right.
+###
+
+## I wanted to do some command line parsing here, but my shell
+## scripting is not really up to it, which is a pity. The end solution
+## to this is probably to do as much of the command liner parsing in
+## Java as possible.
+
+
+## This is the location of the main install directory where Cinema
+## should find all most of its jar files.
+CINEMA_LIB=../lib
+
+## This is the location of any user extensions.
+USER_EXTENSIONS=~/.cinema/ext
+
+VERBOSE=0
+
+# while getopts :L:U:D:V c
+
+# do
+# case $c in
+# L) CINEMA_LIB=$OPTARG;;
+# U) USER_EXTENSIONS=$OPTARG;;
+# V) VERBOSE=1;;
+# ## we want to be able to pass -D options as java virtual
+# ## machine options. This duplicates them so that we can pass
+# ## them before the java class argument. There presence after
+# ## the class as well should not cause any problems and I don't
+# ## know a quick way of removing them.
+# D) JVM_OPTIONS="${JVM_OPTIONS} -D$OPTARG";;
+# ## pass everything else onwards
+# \?) echo parsing unknown $OPTARG $c
+# OTHER_OPTIONS="${OTHER_OPTIONS} -$OPTARG";;
+# esac
+# done
+
+
+## identify the user jars and generate the relevent string
+for jar_file in ${USER_EXTENSIONS}/*.jar
+do
+ user_jars=${user_jars}:$jar_file
+done
+## also let the users have files not in jars
+user_jars=${user_jars}:${USER_EXTENSIONS}
+
+## and the same for cinema jars
+for jar_file in ${CINEMA_LIB}/*.jar
+do
+ cinema_jars=${cinema_jars}:$jar_file
+done
+
+## and finally for any external libraries
+for jar_file in ${CINEMA_LIB}/ext/*.jar
+do
+ ext_jars=${ext_jars}:$jar_file
+done
+
+# classpath
+classpath=${user_jars}${cinema_jars}${ext_jars}
+
+
+##
+## run CINEMA
+##
+COMMAND_LINE="java -classpath ${classpath} ${JVM_OPTIONS} uk.ac.man.bioinf.apps.cinema.Cinema ${OTHER_ARGUMENTS} $*"
+
+## print out the command line if verbose
+if test $VERBOSE -eq 1
+ then
+ echo "Running Cinema as ${COMMAND_LINE}"
+fi
+
+java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS $*
diff --git a/src/uk/ac/man/bioinf/bin/cinema.cygwin b/src/uk/ac/man/bioinf/bin/cinema.cygwin
new file mode 100644
index 0000000..4f87c3c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/bin/cinema.cygwin
@@ -0,0 +1,81 @@
+#!/bin/sh
+
+###
+### Launch script for Cinema.
+###
+### Copyright (c) 2001 Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+
+###
+### This is the definative launch script for Cinema. I have scripts in
+### other languages also, but if they differ in their functionality,
+### all the others are wrong and this one is right.
+###
+
+## Parse the command line. We do not actually want to parse the entire
+## command as most of the work should be done by cinema. Unfortunately
+## some options have to be set before the JVM is launched so we have
+## to do some work here.
+
+
+## This is the location of the main install directory where Cinema
+## should find all most of its jar files.
+CINEMA_LIB=../lib
+
+## This is the location of any user extensions.
+USER_EXTENSIONS=~/.cinema/ext
+
+VERBOSE=1
+
+# while getopts L:U:D:V c
+
+# do
+# case $c in
+# L) CINEMA_LIB=$OPTARG;;
+# U) USER_EXTENSIONS=$OPTARG;;
+# V) VERBOSE=1;;
+# ## we want to be able to pass -D options as java virtual
+# ## machine options. This duplicates them so that we can pass
+# ## them before the java class argument. There presence after
+# ## the class as well should not cause any problems and I don't
+# ## know a quick way of removing them.
+# D) JVM_OPTIONS="${JVM_OPTIONS} -D$OPTARG";;
+# ## pass everything else onwards
+# \?) OTHER_OPTIONS="${OTHER_OPTIONS}-${c}$OPTARG";;
+# esac
+# done
+
+## identify the user jars and generate the relevent string
+for jar_file in ${USER_EXTENSIONS}/*.jar
+do
+ user_jars=${user_jars}";"$jar_file
+done
+
+## and the same for cinema jars
+for jar_file in ${CINEMA_LIB}/*.jar
+do
+ cinema_jars=${cinema_jars}";"$jar_file
+done
+
+
+## and finally for any external libraries
+for jar_file in ${CINEMA_LIB}/ext/*.jar
+do
+ ext_jars=${ext_jars}";"$jar_file
+done
+
+# classpath
+classpath=${user_jars}${cinema_jars}${ext_jars}
+
+
+##
+## run CINEMA
+##
+COMMAND_LINE="java -classpath ${classpath} ${JVM_OPTIONS} uk.ac.man.bioinf.apps.cinema.Cinema ${OTHER_ARGUMENTS}"
+
+## print out the command line if verbose
+if test $VERBOSE -eq 1
+ then
+ echo "Running Cinema as ${COMMAND_LINE}"
+fi
+
+java -classpath ${classpath} uk.ac.man.bioinf.apps.cinema.Cinema $OTHER_ARGUMENTS
diff --git a/src/uk/ac/man/bioinf/bin/cinema.pl b/src/uk/ac/man/bioinf/bin/cinema.pl
new file mode 100644
index 0000000..0f5f991
--- /dev/null
+++ b/src/uk/ac/man/bioinf/bin/cinema.pl
@@ -0,0 +1,78 @@
+#!/usr/bin/perl
+
+
+### This is a launch script for Cinema
+
+
+###
+### This is a direct port of the Cinema sh script which is to be
+### considered the definative version in terms of functionality.
+###
+### This is particularly true in the case of this script as I am a
+### registered member of the perl post-traumatic stress disorder
+### self-help society.
+###
+### Copyright (c) 2001 Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+###
+
+
+
+use Getopt::Std;
+
+my $CINEMA_LIB="../lib";
+my $USER_EXTENSIONS="~/.cinema/ext";
+my $VERBOSE=0;
+my $JVM_OPTIONS;
+
+getopts( 'L:U:D:V' );
+
+
+if( $opt_L ){
+ $CINEMA_LIB = $opt_L;
+}
+
+if( $opt_U ){
+ $USER_EXTENSIONS=$opt_U;
+}
+
+if( $opt_V ){
+ $VERBOSE=$opt_V;
+}
+
+if( $opt_D ){
+ ## I don't think that this will work correctly. Its only going to
+ ## set an single -D option which is a bit of a pain.
+ $JVM_OPTIONS="$JVM_OPTIONS -D$opt_D";
+}
+
+my $jarfile;
+my $user_jars = "";
+my $cinema_jars= "";
+my $ext_jars = "";
+
+
+foreach $jarfile ( glob( "$USER_EXTENSIONS/*jar" ) ){
+ $user_jars.=":$jarfile";
+}
+
+foreach $jarfile ( glob( "$CINEMA_LIB/*jar" ) ){
+ $cinema_jars.=":$jarfile";
+}
+
+foreach $jarfile ( glob( "$CINEMA_LIB/ext/*jar" ) ){
+ $ext_jars.=":$jarfile";
+}
+
+my $classpath="$user_jars$cinema_jars$ext_jars";
+
+if( $VERBOSE ){
+ print "java -classpath $classpath $JVM_OPTIONS uk.ac.man.bioinf.apps.cinema.Cinema @ARGV";
+}
+
+print `java -classpath $classpath $JVM_OPTIONS uk.ac.man.bioinf.apps.cinema.Cinema @ARGV`;
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/build.xml b/src/uk/ac/man/bioinf/build.xml
new file mode 100644
index 0000000..fd816eb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/build.xml
@@ -0,0 +1,333 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<!-- This library is free software; you can redistribute it and/or -->
+<!-- modify it under the terms of the GNU Lesser General Public -->
+<!-- License as published by the Free Software Foundation; either -->
+<!-- version 2.1 of the License, or (at your option) any later version. -->
+
+<!-- This library is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -->
+<!-- Lesser General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU Lesser General Public -->
+<!-- License along with this library; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA -->
+<!-- 02111-1307 USA -->
+
+<project name="bioinf" default="build" basedir="." >
+
+ <!-- Editable properties. These can be modified to the users own
+ requirements, either by editing them in this file, or alternatively
+ by launching ant with the -D options of the form -Ddebug=on -->
+
+ <!-- Provide the option of a properties file. You can use this file
+ to override any of the properties set later on, to customise the
+ build process -->
+ <property name="load.file" value="${user.home}/.ant/bioinf.props" />
+ <property file="${load.file}" />
+
+ <!-- Where to find the route directory of the source hierarchy -->
+ <property name="src" value="../../../.." />
+
+ <!-- The base directory within which to dump everything else -->
+ <property name="builddir" value="${src}/.." />
+
+ <!-- Where should the class files that are produced by put -->
+ <property name="classes" value="${builddir}/classes" />
+
+ <!-- Where should the distributable jar files be generated -->
+ <property name="lib" value="${builddir}/lib" />
+
+ <!-- Where should documentation be kept -->
+ <property name="doc" value="${builddir}/doc" />
+
+ <!-- Where the javadoc files should be generated -->
+ <property name="javadoc" value="${doc}/javadoc" />
+
+ <!-- Where should binary files be kept -->
+ <property name="bin" value="${builddir}/bin" />
+
+ <!-- And the various javadoc options -->
+ <property name="javadoc.link.offline" value="true" />
+ <property name="javadoc.link.location" value="http://java.sun.com/products/jdk/1.2/docs/api/" />
+ <property name="javadoc.package.list.location"
+ value="${src}/uk/ac/man/bioinf/build/" />
+ <property name="javadoc.private" value="false" />
+ <property name="javadoc.packages" value="uk.ac.man.bioinf.*" />
+
+ <!-- Support for texi doclet. Set the first to use -->
+ <property name="javadoc.use.texidoc"/>
+ <property name="javadoc.texidoc.path" value="."/>
+ <property name="javadoc.texi" value="${javadoc}" />
+
+ <!-- External resources. The build process can bring in several
+ external resources, and the position of these are configured here
+ -->
+
+ <!-- Where are the additional jar files required for the compilation -->
+ <property name="ext" value="${classes}/ext" />
+
+ <!-- Where is non-javadoc documentation stored -->
+ <property name="ext-doc" value="${builddir}/ext-doc" />
+
+
+ <!-- Compile with debug on or not -->
+ <property name="debug" value="off" />
+ <property name="exclude" value="**/*Test*" />
+
+ <!-- End user editable properties. You should not edit beyond this
+ point unless you know what you are doing! -->
+
+ <!-- There are four empty directories in the class names, which are
+ a pain to type so this property is the "real" root of the class file
+ hierachy -->
+ <property name="cls-rt" value="uk/ac/man/bioinf" />
+
+
+ <!-- Define the project class path at this point -->
+ <path id="project.class.path">
+ <pathelement location="${classes}" />
+ <fileset dir="${ext}">
+ <include name="**/*.jar" />
+ </fileset>
+
+ </path>
+
+ <target name="prepare" description="Generates the directories required" >
+ <mkdir dir="${classes}" />
+ <mkdir dir="${lib}" />
+ <mkdir dir="${javadoc}" />
+ <mkdir dir="${bin}" />
+ <mkdir dir="${doc}" />
+ <!-- Is there any external documentation? -->
+ <available file="${ext-doc}" property="ext-doc-present" />
+ </target>
+
+ <target name="build" description="Compiles all classes">
+ <javac classpathref="project.class.path"
+ debug="${debug}"
+ srcdir="${src}"
+ destdir="${classes}">
+ <include name="uk/**/*.java" />
+ <exclude name="${exclude}" />
+ </javac>
+ </target>
+
+ <!-- builds a series of jar files for the bioinf package -->
+ <target name="jar" description="Produce a jar file">
+
+
+ <!-- create a series of jar files which are
+ hopefully complete -->
+
+ <!-- First build the util package. This has some utilities that
+ pretty much everything else depends on -->
+ <jar jarfile="${lib}/util.jar" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/debug/**/*.class" />
+ <include name="${cls-rt}/util/**/*.class" />
+ </fileset>
+ </jar>
+
+ <!-- Next the sequence package. Contains the sequence API io
+ methods for this, database access and some analysis -->
+ <jar jarfile="${lib}/sequence.jar" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/analysis/**/*.class" />
+ <include name="${cls-rt}/database/fetch/**/*.class" />
+ <include name="${cls-rt}/io/**/*.class" />
+ <include name="${cls-rt}/sequence/**/*.class" />
+ </fileset>
+ </jar>
+
+ <!-- now the graph package. This should probably be repackaged
+ into the gui package -->
+ <jar jarfile="${lib}/graph.jar" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/graph/**/*.class" />
+ </fileset>
+ </jar>
+
+ <!-- Now the gui package. Contains graphics components -->
+ <jar jarfile="${lib}/gui.jar" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/gui/**/*.class" />
+ </fileset>
+ </jar>
+
+ <!-- The mxc module architecture. Probably the XML package should
+ be repackaged at some time as a subpackage of module. -->
+ <jar jarfile="${lib}/mxc.jar">
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/module/**/*.class" />
+ <include name="${cls-rt}/apps/xml/**/*.class" />
+ </fileset>
+ </jar>
+
+ <!-- app support -->
+ <jar jarfile="${lib}/app_support.jar" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/apps/systemevents/**/*.class" />
+ <include name="${cls-rt}/apps/optionable/**/*.class" />
+ <include name="${cls-rt}/apps/invoker/**/*.class" />
+ </fileset>
+ </jar>
+
+ <jar jarfile="${lib}/emboss.jar" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/emboss/**/*.class" />
+ </fileset>
+ </jar>
+
+ <!-- The Cinema specific classes -->
+ <jar jarfile="${lib}/cinema.jar"
+ manifest="${src}/${cls-rt}/build/manifest" >
+ <fileset dir="${classes}" >
+ <include name="${cls-rt}/apps/cinema/**/*.class" />
+ </fileset>
+ <!-- Cinema includes resource files. These are normally kept in
+ the source directories. -->
+ <fileset dir="${src}" >
+ <include name="uk/ac/man/bioinf/apps/cinema/resources/**" />
+ <exclude name="*.java" />
+ </fileset>
+ </jar>
+
+ <!-- package up all of the source into one place -->
+ <jar jarfile="${lib}/src.jar">
+ <fileset dir="${src}" >
+ <include name="uk/" />
+ </fileset>
+ </jar>
+
+ </target>
+
+ <target name="clean_safety" description="Protection against clean"
+ if="clean.safety.check">
+ <fail message="The property clean.safety.check has been set,
+probably in the file ${load.file}, which disallows running the
+clean target. Perhaps you want class_clean instead?" >
+ </fail>
+ </target>
+
+ <target name="clean" description="Delete all produced files"
+ depends="clean_safety">
+ <!-- delete the class files which have been produced -->
+ <delete dir="${classes}" />
+ <!-- delete the jar files -->
+ <delete file="${lib}/*.jar" />
+ <!-- delete the documentation -->
+ <delete dir="${doc}" />
+ <!-- remove the binaries -->
+ <delete dir="${bin}" />
+ </target>
+
+ <target name="class_clean" description="Delete the class files">
+ <!-- delete the class files which have been produced -->
+ <delete>
+ <fileset dir="${classes}/uk" includes="**/*.class" />
+ </delete>
+ </target>
+
+ <target name="javadoc" depends="javadoc_normal,javadoc_texi"
+ description="Runs javadoc" />
+
+ <target name="javadoc_normal"
+ description="Makes all the javadoc using normal doclet"
+ unless="javadoc.use.texidoc"
+ >
+ <javadoc sourcepath="${src}"
+ destdir="${javadoc}"
+ private="${javadoc.private}"
+ packagenames="${javadoc.packages}" >
+ <link offline="${javadoc.link.offline}"
+ href="${javadoc.link.location}"
+ packagelistLoc="${javadoc.package.list.location}"
+ />
+ <group title="Sequence Packages"
+ packages="uk.ac.man.bioinf.sequence*" />
+ <group title="Gui Packages"
+ packages="uk.ac.man.bioinf.gui*" />
+ <group title="Cinema"
+ packages="uk.ac.man.bioinf.apps.cinema*" />
+ </javadoc>
+ </target>
+
+ <target name="javadoc_texi" if="javadoc.use.texidoc"
+ description="Javadocs using the texi doclet" >
+ <!-- <javadoc sourcepath="${src}"
+ private="${javadoc.private}"
+ packagenames="${javadoc.packages}" >
+ <doclet name="gnu.texidoclet.Driver"
+ path="${javadoc.texidoc.path}/TexiDoclet.jar" >
+ <param name="-d" value="${javadoc.TeX}" />
+ </doclet>
+ </javadoc>
+ -->
+ <execon executable="makeinfo" parallel="yes">
+ <fileset dir="${javadoc.texi}">
+ <patternset>
+ <include name="**/*.texi"/>
+ </patternset>
+ </fileset>
+ </execon>
+ <copy file="${javadoc.package.list.location}/dir"
+ todir="${javadoc.texi}" />
+ </target>
+
+ <target name="include_external"
+ description="Includes external resources"
+ depends="prepare,include_external_documentation" >
+ <mkdir dir="${lib}/ext" />
+ <mkdir dir="${builddir}/doc" />
+ <!-- copy the external jar files -->
+ <copy todir="${lib}/ext" >
+ <fileset dir="${ext}">
+ <include name="**/*.jar" />
+ </fileset>
+ </copy>
+ </target>
+
+ <target name="include_external_documentation"
+ description="Includes external documentation if it is available"
+ depends="prepare"
+ if="ext-doc-present" >
+ <copy todir="${doc}" >
+ <fileset dir="${ext-doc}/" />
+ </copy>
+ </target>
+
+ <target name="shuffle"
+ description="Shuffles a few files around" >
+ <!-- this main README needs to be at the top level -->
+ <echo message="Copy should be to ${builddir} from ${doc}/README" />
+ <move todir="${builddir}" >
+ <fileset dir="${doc}" >
+ <include name ="README*" />
+ </fileset>
+ </move>
+ <!-- The change log needs to moved upwards -->
+ <copy tofile="${doc}/cinema-changes.html"
+ file="${src}/${cls-rt}/apps/cinema/changes.html"/>
+ <!-- Copy the binaries files into their appropriate directories -->
+ <copy todir="${bin}">
+ <fileset dir="${src}/${cls-rt}/bin">
+ <include name="**" />
+ </fileset>
+ </copy>
+ <!-- Make them executable if it makes sense on the OS -->
+ <chmod dir="${bin}" perm="a+x" includes="**" />
+ </target>
+
+ <target name="dist_build" description="Build all the executables"
+ depends="prepare,build,jar,include_external,shuffle" />
+
+
+ <target name="all" description="Build everything from scratch"
+ depends="clean,prepare,dist_build,javadoc" />
+</project>
+
+
+
+
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/build/cinema-build.xml b/src/uk/ac/man/bioinf/build/cinema-build.xml
new file mode 100644
index 0000000..2c43465
--- /dev/null
+++ b/src/uk/ac/man/bioinf/build/cinema-build.xml
@@ -0,0 +1,180 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+
+<!-- This library is free software; you can redistribute it and/or -->
+<!-- modify it under the terms of the GNU Lesser General Public -->
+<!-- License as published by the Free Software Foundation; either -->
+<!-- version 2.1 of the License, or (at your option) any later version. -->
+
+<!-- This library is distributed in the hope that it will be useful, -->
+<!-- but WITHOUT ANY WARRANTY; without even the implied warranty of -->
+<!-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -->
+<!-- Lesser General Public License for more details. -->
+
+<!-- You should have received a copy of the GNU Lesser General Public -->
+<!-- License along with this library; if not, write to the Free Software -->
+<!-- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -->
+
+
+
+
+<!-- This build file is for building and installing current versions -->
+<!-- of Cinema. The actual build is carried out by a different build -->
+<!-- file. All that this script does is get hold of the source in the -->
+<!-- first place from which the main build script works. There are -->
+<!-- three main ways of doing this. The first is to get a tagged -->
+<!-- version in the CVS repository. This is the normal way to build -->
+<!-- distributable files. The second way is to get the most recent CVS -->
+<!-- files, and build from these. And finally the source can be -->
+<!-- recovered directly from your own working copy and build from -->
+<!-- there. The root directory of the build process reflects which of -->
+<!-- these options has been taken. -->
+<project name="cinema" default="build-cinema" basedir=".">
+
+ <property name="cinema-load-file" value="${user.home}/.ant/cinema.props" />
+ <property file="${cinema-load-file}" />
+ <!-- This is the name of the subtarget to build having gathered the
+ source together. The default "all" does everything, but "dist_build"
+ just builds the executables (no documentation) and does not clean
+ first, so its a good choice if you are modifying the build files, as
+ its much quicker -->
+ <property name="sub-target" value="all" />
+
+ <!-- This is the number of the latest cinema release -->
+ <property name="cinema.latest.release" value="3_0_23" />
+
+ <!-- This is the location of source files if cinema-latest is being
+ installed -->
+ <property name="latest.source" value="/home/phillord/src/java" />
+ <property name="src" value="src" />
+ <property name="prefix" value="/usr/local" />
+ <property name="ext" value="${prefix}/lib/cinema/lib/ext"/>
+ <property name="ext-doc" value="${src}/doc" />
+
+ <target name = "prepare"
+ description="Prepares the directory structure that is needed" >
+ <mkdir dir="${builddir}" />
+ <mkdir dir="${builddir}/${src}" />
+ </target>
+
+ <!-- Some of the source is a little scary, and at the moment we do
+ not want on general release. So delete it here. -->
+ <target name="strip" description="Removes some of the source"
+ unless="dont.strip.dubious.source">
+ <delete dir="${builddir}/${src}/uk/ac/man/bioinf/biowarehouse" />
+ <delete dir="${builddir}/${src}/uk/ac/man/bioinf/graph" />
+ <delete dir="${builddir}/${src}/uk/ac/man/bioinf/gdbw" />
+ <delete dir="${builddir}/${src}/uk/ac/man/bioinf/database/printswrapper" />
+ <delete dir="${builddir}/${src}/uk/ac/man/bioinf/apps/cinema/temp" />
+ </target>
+
+ <target name="build-cinema"
+ description="Builds the latest cinema from the CVS tree" >
+ <!-- This sets up the build directory for what follows -->
+ <property name="buildname" value="cvs" />
+ <property name="builddir" value="${basedir}/cinema-${buildname}" />
+ <!-- Having set the build directory we can build the correct directory strucutre -->
+ <antcall target="prepare" />
+ <!-- check out everything -->
+ <cvs cvsRoot=":pserver:anon at proline.sbc.man.ac.uk:/nfs/cvs"
+ package="bioinf"
+ dest="${builddir}/${src}"
+ command="checkout" />
+ <!-- build everything -->
+ <antcall target="package" />
+ </target>
+
+ <target name="install-cinema"
+ depends="build-cinema"
+ description="Install Cinema from the CVS tree" >
+ <!-- install -->
+ <copy file="cinema.jar" toFile="${prefix}/lib/cinema/cinema.jar" />
+ </target>
+
+ <target name="build-cinema-latest"
+ description="Build Cinema from the current source version as cinema-latest">
+ <property name="buildname" value="latest" />
+ <property name="builddir" value="${basedir}/cinema-${buildname}" />
+ <antcall target = "prepare" />
+ <copy todir="${builddir}/${src}">
+ <fileset dir="${latest.source}">
+ <include name="uk/**" />
+ </fileset>
+ </copy>
+ <!-- build everything -->
+ <antcall target="package" />
+ </target>
+
+ <target name="install-cinema-latest"
+ depends="build-cinema-latest"
+ description="Install Cinema from the CVS tree" >
+ <!-- install -->
+ <copy file="cinema.jar" toFile="${prefix}/lib/cinema/cinema.jar" />
+ </target>
+
+ <target name="build-cinema-release"
+ description="Build Cinema as a given release">
+ <property name="buildname" value="${cinema.latest.release}" />
+ <property name="builddir" value="${basedir}/cinema-${buildname}" />
+ <antcall target="prepare" />
+ <!-- check out everything -->
+ <cvs cvsRoot=":pserver:anon at proline.sbc.man.ac.uk:/nfs/cvs"
+ package="bioinf"
+ dest="${builddir}/${src}"
+ tag="release-${cinema.latest.release}"
+ command="checkout" />
+ <!-- Produce the distributables -->
+ <antcall target="package" />
+ </target>
+
+ <target name="install-cinema-release"
+ depends="build-cinema-release"
+ description="Install Cinema as a given release">
+ <copy file="cinema.jar"
+ toFile="${prefix}/lib/cinema/cinema-${cinema.latest.release.tag}.jar"
+ />
+ </target>
+
+ <target name="build"
+ depends="strip"
+ description="Runs the build" >
+ <ant antfile="${builddir}/${src}/uk/ac/man/bioinf/build.xml"
+ dir="${builddir}"
+ target="${sub-target}" >
+ <property name="ext-doc" value="${ext-doc}" />
+ </ant>
+
+ </target>
+
+ <!-- This target produces the distributable archives. Two archives
+ are produced, one as a tar.gz, and one zip file. This should
+ probably be modified latter to give a source, and a distribution
+ build. I should probably also produce a distribution without the
+ various extension jars included -->
+ <target name="package" depends="build"
+ description="Packages the build up into distributable archives" >
+ <!-- Build the tar files -->
+ <tar longfile="gnu"
+ tarfile="cinema-${buildname}.tar"
+ >
+ <tarfileset dir="${basedir}">
+ <include name="cinema-${buildname}/**" />
+ <exclude name="cinema-${buildname}/bin/**" />
+ </tarfileset>
+ <tarfileset dir ="${basedir}" mode="755">
+ <include name="cinema-${buildname}/bin/**" />
+ </tarfileset>
+ </tar>
+ <gzip zipfile="cinema-${buildname}.tar.gz"
+ src="cinema-${buildname}.tar" />
+ <delete file="cinema-${buildname}.tar" />
+ <!-- Build the zip files -->
+ <zip zipfile="cinema-${buildname}.zip"
+ basedir="${basedir}"
+ includes="cinema-${buildname}/**" />
+ </target>
+</project>
+
+
+
+
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/build/manifest b/src/uk/ac/man/bioinf/build/manifest
new file mode 100644
index 0000000..2180273
--- /dev/null
+++ b/src/uk/ac/man/bioinf/build/manifest
@@ -0,0 +1,2 @@
+Class-Path: app_support.jar gui.jar mxc.jar sequence.jar util.jar ext/gnu-getopt.jar ext/xerces.jar ext/jakarta-regexp.jar
+Main-Class: uk.ac.man.bioinf.apps.cinema.Cinema
diff --git a/src/uk/ac/man/bioinf/build/package-list b/src/uk/ac/man/bioinf/build/package-list
new file mode 100644
index 0000000..407d0d7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/build/package-list
@@ -0,0 +1,59 @@
+java.applet
+java.awt
+java.awt.color
+java.awt.datatransfer
+java.awt.dnd
+java.awt.event
+java.awt.font
+java.awt.geom
+java.awt.im
+java.awt.image
+java.awt.image.renderable
+java.awt.print
+java.beans
+java.beans.beancontext
+java.io
+java.lang
+java.lang.ref
+java.lang.reflect
+java.math
+java.net
+java.rmi
+java.rmi.activation
+java.rmi.dgc
+java.rmi.registry
+java.rmi.server
+java.security
+java.security.acl
+java.security.cert
+java.security.interfaces
+java.security.spec
+java.sql
+java.text
+java.util
+java.util.jar
+java.util.zip
+javax.accessibility
+javax.swing
+javax.swing.border
+javax.swing.colorchooser
+javax.swing.event
+javax.swing.filechooser
+javax.swing.plaf
+javax.swing.plaf.basic
+javax.swing.plaf.metal
+javax.swing.plaf.multi
+javax.swing.table
+javax.swing.text
+javax.swing.text.html
+javax.swing.text.html.parser
+javax.swing.text.rtf
+javax.swing.tree
+javax.swing.undo
+org.omg.CORBA
+org.omg.CORBA.DynAnyPackage
+org.omg.CORBA.ORBPackage
+org.omg.CORBA.portable
+org.omg.CORBA.TypeCodePackage
+org.omg.CosNaming
+org.omg.CosNaming.NamingContextPackage
diff --git a/src/uk/ac/man/bioinf/build/project-ext.dtd b/src/uk/ac/man/bioinf/build/project-ext.dtd
new file mode 100644
index 0000000..0924399
--- /dev/null
+++ b/src/uk/ac/man/bioinf/build/project-ext.dtd
@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+
+<!--
+ Copyright (c) 2000 Michel CASABIANCA. All Rights Reserved.
+
+ Permission to use, copy, modify, and distribute this software and its
+ documentation for any purpose and without fee or royalty is hereby
+ granted, provided that both the above copyright notice and this
+ permission notice appear in all copies of the software and
+ documentation or portions thereof, including modifications, that you
+ make.
+
+ THIS SOFTWARE IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS MAKE NO
+ REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE,
+ BUT NOT LIMITATION, COPYRIGHT HOLDERS MAKE NO REPRESENTATIONS OR
+ WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR
+ THAT THE USE OF THE SOFTWARE OR DOCUMENTATION WILL NOT INFRINGE ANY
+ THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS.
+ COPYRIGHT HOLDERS WILL BEAR NO LIABILITY FOR ANY USE OF THIS SOFTWARE
+ OR DOCUMENTATION.
+-->
+
+<!-- project ext DTD for Ant -->
+<!-- 2000-04-03 -->
+
+<!ENTITY % ext "| xt">
+
+<!ELEMENT xt EMPTY>
+<!ATTLIST xt
+ xml CDATA #REQUIRED
+ xsl CDATA #REQUIRED
+ out CDATA #REQUIRED>
+
+
diff --git a/src/uk/ac/man/bioinf/build/project.dtd b/src/uk/ac/man/bioinf/build/project.dtd
new file mode 100644
index 0000000..7320ac2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/build/project.dtd
@@ -0,0 +1,273 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+
+<!--
+ Copyright (c) 2000 Michel CASABIANCA. All Rights Reserved.
+
+ Permission to use, copy, modify, and distribute this software and its
+ documentation for any purpose and without fee or royalty is hereby
+ granted, provided that both the above copyright notice and this
+ permission notice appear in all copies of the software and
+ documentation or portions thereof, including modifications, that you
+ make.
+
+ THIS SOFTWARE IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS MAKE NO
+ REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED. BY WAY OF EXAMPLE,
+ BUT NOT LIMITATION, COPYRIGHT HOLDERS MAKE NO REPRESENTATIONS OR
+ WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE OR
+ THAT THE USE OF THE SOFTWARE OR DOCUMENTATION WILL NOT INFRINGE ANY
+ THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS.
+ COPYRIGHT HOLDERS WILL BEAR NO LIABILITY FOR ANY USE OF THIS SOFTWARE
+ OR DOCUMENTATION.
+-->
+
+<!-- project DTD for Ant -->
+<!-- 2000-04-03 -->
+
+<!ENTITY % ext-file SYSTEM "project-ext.dtd">
+%ext-file;
+
+<!ELEMENT project (target | property)*>
+<!ATTLIST project
+ name CDATA #REQUIRED
+ default CDATA #REQUIRED
+ basedir CDATA #REQUIRED>
+
+<!ELEMENT target (ant | available | chmod | copydir | copyfile |
+ cvs | delete | deltree | echo | exec | expand |
+ filter | get | gzip | fixcrlf | jar | java |
+ javac | javadoc | javadoc2 | keysubst | mkdir |
+ property | rename | replace | rmic | tar |
+ taskdef | tstamp | zip %ext;)*>
+<!ATTLIST target
+ name CDATA #REQUIRED
+ depends CDATA #IMPLIED
+ if CDATA #IMPLIED>
+
+<!ELEMENT property EMPTY>
+<!ATTLIST property
+ name CDATA #IMPLIED
+ value CDATA #IMPLIED
+ resource CDATA #IMPLIED
+ file CDATA #IMPLIED>
+
+<!ELEMENT ant EMPTY>
+<!ATTLIST ant
+ antfile CDATA #IMPLIED
+ dir CDATA #REQUIRED
+ target CDATA #IMPLIED>
+
+<!ELEMENT available EMPTY>
+<!ATTLIST available
+ property CDATA #REQUIRED
+ classname CDATA #REQUIRED
+ resource CDATA #REQUIRED
+ file CDATA #REQUIRED>
+
+<!ELEMENT chmod EMPTY>
+<!ATTLIST chmod
+ src CDATA #REQUIRED
+ perm CDATA #REQUIRED>
+
+<!ELEMENT copydir EMPTY>
+<!ATTLIST copydir
+ src CDATA #REQUIRED
+ dest CDATA #REQUIRED
+ ignore CDATA #IMPLIED
+ includes CDATA #IMPLIED
+ excludes CDATA #IMPLIED
+ defaultexcludes CDATA #IMPLIED
+ filtering CDATA #IMPLIED>
+
+<!ELEMENT copyfile EMPTY>
+<!ATTLIST copyfile
+ src CDATA #REQUIRED
+ dest CDATA #REQUIRED
+ filtering CDATA #IMPLIED>
+
+<!ELEMENT cvs EMPTY>
+<!ATTLIST cvs
+ cvsRoot CDATA #REQUIRED
+ dest CDATA #REQUIRED
+ package CDATA #REQUIRED
+ tag CDATA #IMPLIED>
+
+<!ELEMENT delete EMPTY>
+<!ATTLIST delete
+ file CDATA #REQUIRED>
+
+<!ELEMENT deltree EMPTY>
+<!ATTLIST deltree
+ dir CDATA #REQUIRED>
+
+<!ELEMENT echo EMPTY>
+<!ATTLIST echo
+ message CDATA #REQUIRED>
+
+<!ELEMENT exec EMPTY>
+<!ATTLIST exec
+ command CDATA #REQUIRED
+ dir CDATA #REQUIRED
+ os CDATA #IMPLIED
+ output CDATA #REQUIRED>
+
+<!ELEMENT expand EMPTY>
+<!ATTLIST expand
+ src CDATA #REQUIRED
+ dest CDATA #REQUIRED>
+
+<!ELEMENT filter EMPTY>
+<!ATTLIST filter
+ token CDATA #REQUIRED
+ value CDATA #REQUIRED>
+
+<!ELEMENT get EMPTY>
+<!ATTLIST get
+ src CDATA #REQUIRED
+ dest CDATA #REQUIRED
+ verbose CDATA #IMPLIED>
+
+<!ELEMENT gzip EMPTY>
+<!ATTLIST gzip
+ src CDATA #REQUIRED
+ zipfile CDATA #REQUIRED>
+
+<!ELEMENT fixcrlf EMPTY>
+<!ATTLIST fixcrlf
+ srcdir CDATA #REQUIRED
+ destDir CDATA #IMPLIED
+ includes CDATA #IMPLIED
+ excludes CDATA #IMPLIED
+ cr CDATA #IMPLIED
+ tab CDATA #IMPLIED
+ eof CDATA #IMPLIED>
+
+<!ELEMENT jar EMPTY>
+<!ATTLIST jar
+ jarfile CDATA #REQUIRED
+ basedir CDATA #REQUIRED
+ items CDATA #IMPLIED
+ ignore CDATA #IMPLIED
+ includes CDATA #IMPLIED
+ excludes CDATA #IMPLIED
+ defaultexcludes CDATA #IMPLIED
+ manifest CDATA #IMPLIED>
+
+<!ELEMENT java EMPTY>
+<!ATTLIST java
+ classname CDATA #REQUIRED
+ args CDATA #IMPLIED
+ fork CDATA #IMPLIED
+ jvmargs CDATA #IMPLIED>
+
+<!ELEMENT javac EMPTY>
+<!ATTLIST javac
+ srcdir CDATA #REQUIRED
+ destdir CDATA #REQUIRED
+ includes CDATA #IMPLIED
+ excludes CDATA #IMPLIED
+ defaultexcludes CDATA #IMPLIED
+ classpath CDATA #IMPLIED
+ bootclasspath CDATA #IMPLIED
+ extdirs CDATA #IMPLIED
+ debug CDATA #IMPLIED
+ optimize CDATA #IMPLIED
+ deprecation CDATA #IMPLIED
+ filtering CDATA #IMPLIED>
+
+<!ELEMENT javadoc EMPTY>
+<!ATTLIST javadoc
+ sourcepath CDATA #REQUIRED
+ destdir CDATA #REQUIRED
+ sourcefiles CDATA #IMPLIED
+ packagenames CDATA #IMPLIED
+ classpath CDATA #IMPLIED
+ bootclasspath CDATA #IMPLIED
+ extdirs CDATA #IMPLIED
+ overview CDATA #IMPLIED
+ public CDATA #IMPLIED
+ protected CDATA #IMPLIED
+ package CDATA #IMPLIED
+ private CDATA #IMPLIED
+ old CDATA #IMPLIED
+ verbose CDATA #IMPLIED
+ locale CDATA #IMPLIED
+ encoding CDATA #IMPLIED
+ version CDATA #IMPLIED
+ use CDATA #IMPLIED
+ author CDATA #IMPLIED
+ splitindex CDATA #IMPLIED
+ windowtitle CDATA #IMPLIED
+ doctitle CDATA #IMPLIED
+ header CDATA #IMPLIED
+ footer CDATA #IMPLIED
+ bottom CDATA #IMPLIED
+ link CDATA #IMPLIED
+ linkoffline CDATA #IMPLIED
+ group CDATA #IMPLIED
+ nodedeprecated CDATA #IMPLIED
+ nodedeprecatedlist CDATA #IMPLIED
+ notree CDATA #IMPLIED
+ noindex CDATA #IMPLIED
+ nohelp CDATA #IMPLIED
+ nonavbar CDATA #IMPLIED
+ serialwarn CDATA #IMPLIED
+ helpfile CDATA #IMPLIED
+ stylesheetfile CDATA #IMPLIED
+ charset CDATA #IMPLIED
+ docencoding CDATA #IMPLIED>
+
+<!ELEMENT keysubst EMPTY>
+<!ATTLIST keysubst
+ src CDATA #REQUIRED
+ dest CDATA #REQUIRED
+ sep CDATA #IMPLIED
+ keys CDATA #REQUIRED>
+
+<!ELEMENT mkdir EMPTY>
+<!ATTLIST mkdir
+ dir CDATA #REQUIRED>
+
+<!ELEMENT rename EMPTY>
+<!ATTLIST rename
+ src CDATA #REQUIRED
+ dest CDATA #REQUIRED
+ replace CDATA #IMPLIED>
+
+<!ELEMENT replace EMPTY>
+<!ATTLIST replace
+ file CDATA #REQUIRED
+ token CDATA #REQUIRED
+ value CDATA #IMPLIED>
+
+<!ELEMENT rmic EMPTY>
+<!ATTLIST rmic
+ base CDATA #REQUIRED
+ classname CDATA #REQUIRED
+ filtering CDATA #IMPLIED>
+
+<!ELEMENT tar EMPTY>
+<!ATTLIST tar
+ tarfile CDATA #REQUIRED
+ basedir CDATA #REQUIRED
+ includes CDATA #IMPLIED
+ excludes CDATA #IMPLIED
+ defaultexcludes CDATA #IMPLIED>
+
+<!ELEMENT taskdef EMPTY>
+<!ATTLIST taskdef
+ name CDATA #REQUIRED
+ classname CDATA #REQUIRED>
+
+<!ELEMENT tstamp EMPTY>
+
+<!ELEMENT zip EMPTY>
+<!ATTLIST zip
+ zipfile CDATA #REQUIRED
+ basedir CDATA #REQUIRED
+ items CDATA #IMPLIED
+ ignore CDATA #IMPLIED
+ includes CDATA #IMPLIED
+ excludes CDATA #IMPLIED
+ defaultexcludes CDATA #IMPLIED>
+
+
diff --git a/src/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.java b/src/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.java
new file mode 100644
index 0000000..2d77117
--- /dev/null
+++ b/src/uk/ac/man/bioinf/database/fetch/ExpasySequenceRetriever.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.database.fetch; // Package name inserted by JPack
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URL;
+import uk.ac.man.bioinf.io.NarrowedInputStream;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.SequenceInputParser;
+import uk.ac.man.bioinf.io.parsers.FastaSequenceParser;
+import uk.ac.man.bioinf.sequence.Sequence;
+
+
+/**
+ * ExpasySequenceRetriever.java
+ *
+ * Retrieves Swissprot sequence from Expasy.
+ *
+ * For this class to work it makes an HTTP connection, and it
+ * therefore works a lot better, if the HTTP proxy has been set
+ * correctly. java -DproxySet=true -DproxyHost=proxyhost
+ * [-DproxyPort=portNumber] is a good way to do this.
+ *
+ *
+ * It also makes explicit use of the URL format used at EXPASY, and I
+ * have no idea how stable these are.
+ *
+ * I am retrieving
+ *
+ * Created: Thu Feb 8 17:22:05 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: ExpasySequenceRetriever.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ExpasySequenceRetriever implements SequenceRetriever
+{
+ private String url;
+ private SequenceInputParser parse;
+
+ public ExpasySequenceRetriever() throws IOException
+ {
+ this( "http://ch.expasy.org" );
+ }
+
+ public ExpasySequenceRetriever( String baseURL ) throws IOException
+ {
+ url = baseURL + "/cgi-bin/get-sprot-fasta?";
+ this.parse = new FastaSequenceParser();
+ }
+
+ public Sequence retrieveSequence( String swissprot, ParserExceptionHandler exp ) throws IOException
+ {
+ return parse.parse
+ ( new InputStreamReader( retrieveSequenceStream( swissprot ) ), exp );
+ }
+
+ public InputStream retrieveSequenceStream( String swissprot ) throws IOException
+ {
+ // the URL given is to a page with fasta format sequences. It has
+ // other crap on it as well, but the sequence is the only thing in
+ // a <PRE> tag so this should retrieve it.
+ return new BufferedInputStream
+ ( new NarrowedInputStream
+ ( (new URL( url + swissprot ).openStream() ),
+ "<PRE>".getBytes(), "</PRE>".getBytes() ) );
+ }
+
+ public void close()
+ {
+ }
+
+ public void dispose()
+ {
+ }
+
+}
+/*
+ * ChangeLog
+ * $Log: ExpasySequenceRetriever.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:39:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.java b/src/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.java
new file mode 100644
index 0000000..5376e0c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/database/fetch/FetchSequenceBySwissProtID.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.database.fetch; // Package name inserted by JPack
+
+
+/**
+ * FetchSequenceBySwissProtID.java
+ *
+ * This class fetchs a
+ * Created: Wed Feb 7 14:58:40 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: FetchSequenceBySwissProtID.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class FetchSequenceBySwissProtID
+{
+
+ public FetchSequenceBySwissProtID()
+ {
+
+ }
+
+} // FetchSequenceBySwissProtID
+
+
+
+/*
+ * ChangeLog
+ * $Log: FetchSequenceBySwissProtID.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:39:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/database/fetch/SequenceRetriever.java b/src/uk/ac/man/bioinf/database/fetch/SequenceRetriever.java
new file mode 100644
index 0000000..f688713
--- /dev/null
+++ b/src/uk/ac/man/bioinf/database/fetch/SequenceRetriever.java
@@ -0,0 +1,68 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.database.fetch; // Package name inserted by JPack
+import java.io.IOException;
+import java.io.InputStream;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.sequence.Sequence;
+
+
+/**
+ * SequenceRetriever.java
+ *
+ *
+ * Created: Thu Feb 8 16:42:01 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceRetriever.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface SequenceRetriever
+{
+ public Sequence retrieveSequence( String accession, ParserExceptionHandler exp ) throws IOException;
+
+ public InputStream retrieveSequenceStream( String accession ) throws IOException;
+
+ public void close() throws IOException;
+
+ public void dispose() throws IOException;
+} // SequenceRetriever
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceRetriever.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:39:49 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/debug/AbstractDebug.java b/src/uk/ac/man/bioinf/debug/AbstractDebug.java
new file mode 100644
index 0000000..460359b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/AbstractDebug.java
@@ -0,0 +1,92 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+
+
+/**
+ * AbstractDebug.java
+ *
+ *
+ * Created: Wed Mar 1 22:22:22 2000
+ *
+ * @author Phillip Lord
+ * @version
+ */
+
+public abstract class AbstractDebug implements DebugInterface
+{
+ public abstract void message( Class cla, String message );
+ public abstract void throwable( Class cla, Throwable th );
+
+
+
+ public void message( Object obj, String message )
+ {
+ message( obj.getClass(), message );
+ }
+
+ public void message( Object obj, Object message )
+ {
+ message( obj, message.toString() );
+ }
+
+ public void message( Class cla, Object message )
+ {
+ message( cla, message.toString() );
+ }
+
+ public void throwable( Object obj, Throwable th )
+ {
+ throwable( obj.getClass(), th );
+ }
+
+ public void both( Object obj, String message, Throwable th )
+ {
+ message( obj, message );
+ throwable( obj, th );
+ }
+
+ public void both( Class cla, String message, Throwable th )
+ {
+ message( cla, message );
+ throwable( cla, th );
+ }
+
+ public void both( Object obj, Object message, Throwable th )
+ {
+ message( obj, message );
+ throwable( obj, th );
+ }
+
+ public void both( Class cla, Object message, Throwable th )
+ {
+ message( cla, message );
+ throwable( cla, th );
+ }
+}// AbstractDebug
diff --git a/src/uk/ac/man/bioinf/debug/Debug.java b/src/uk/ac/man/bioinf/debug/Debug.java
new file mode 100644
index 0000000..8296267
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/Debug.java
@@ -0,0 +1,210 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+
+
+/**
+ * Debug.java
+ *
+ * This forms the basis of the Debugging architecture. All debugging
+ * statements go through static methods of this class, but what is to
+ * be done with these statements is delegated to an instance of
+ * DebugInterface.
+ *
+ * This instance can be set by naming the class on the command line
+ * as the debug.debug property, or programmatically with the
+ * setInstance() methods. If this represents a change (rather than the
+ * first time the instance is set) both the old and the new instances
+ * are informed what is going on, and about each other so that Debug
+ * logs can be traced.
+ *
+ * If there is a problem with the initiation of the debug class the
+ * default is used, and information is dumped to System.out. What else
+ * can you do under such circumstances?
+ *
+ * Created: Wed Mar 1 21:59:20 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Debug.java,v 1.7 2001/05/08 15:50:47 lord Exp $
+ */
+
+public class Debug
+{
+ /**
+ * This is the main switch variable. It if is set to true before the
+ * compile then any assertions or debug statements within the code
+ * will be left in place, and will impose a runtime penalty. If it
+ * is set to false, before the compile then those assertions will be
+ * optimised away.
+ */
+ public static final boolean debug = false;
+ private static DebugInterface inst;
+
+ static
+ {
+ if( System.getProperty( "debug.debug" ) == null ){
+ // this is a weird way of doing things, but its type safe!!!!
+ setInstance( DefaultDebug.class.getName() );
+ }
+ else{
+ setInstance( "uk.ac.man.bioinf.debug.Debug" + System.getProperty( "debug.debug" ) );
+ }
+ }
+
+ public static void setInstance( DebugInterface deb )
+ {
+ try{
+ DebugInterface old = inst;
+ if( inst != null && debug ){
+ inst.message( null, "DEBUG: Replacing debug instance with instance of " +
+ deb.getClass().getName() );
+ }
+
+ inst = deb;
+ if( old != null && debug ){
+ inst.message( null, "DEBUG: Old Debug instance of class " +
+ old.getClass().getName() + " replaced" );
+ }
+ if( debug ){
+ inst.message( null, "DEBUG: Debug instance of class " +
+ deb.getClass().getName() + " installed" );
+ }
+ }
+ catch( Exception exp ){
+ System.out.println( "ERROR: There is a difficulty loading the debug class "
+ + deb.getClass().getName() );
+ exp.printStackTrace();
+ System.out.println( "ERROR: Using the default debug class instead" );
+ setInstance( DefaultDebug.class.getName() );
+ }
+ }
+
+ public static void setInstance( String debugClass )
+ {
+ try{
+ Class debug = Class.forName( debugClass );
+ setInstance
+ ( (DebugInterface)debug.newInstance() );
+ }
+ catch( ClassNotFoundException cnf ){
+ System.out.println( "ERROR: Debug Class Not Found. Refer to documentation for possible values" );
+ System.out.println( "ERROR: Using the default debug class instead" );
+ setInstance( DefaultDebug.class.getName() );
+ }
+ catch( Exception exp ){
+ System.out.println( "ERROR: There is a difficulty loading the debug class " + debugClass );
+ System.out.println( "ERROR: Using the default debug class instead" );
+ setInstance( DefaultDebug.class.getName() );
+ }
+ }
+
+ public static DebugInterface getInstance()
+ {
+ return inst;
+ }
+
+ public static void message( Object obj, String message )
+ {
+ inst.message( obj, message );
+ }
+
+ public static void message( Object obj, Object message )
+ {
+ inst.message( obj, message );
+ }
+
+ public static void message( Class cla, String message )
+ {
+ inst.message( cla, message );
+ }
+
+ public static void message( Class cla, Object message )
+ {
+ inst.message( cla, message );
+ }
+
+ public static void throwable( Object obj, Throwable th )
+ {
+ inst.throwable( obj, th );
+ }
+
+ public static void throwable( Class cla, Throwable th )
+ {
+ inst.throwable( cla, th );
+ }
+
+ public static void both( Object obj, String message, Throwable th )
+ {
+ inst.both( obj, message, th );
+ }
+
+ public static void both( Class cla, String message, Throwable th )
+ {
+ inst.both( cla, message, th );
+ }
+
+ public static void both( Object obj, Object message, Throwable th )
+ {
+ inst.both( obj, message, th );
+ }
+
+ public static void both( Class cla, Object message, Throwable th )
+ {
+ inst.both( cla, message, th );
+ }
+}// Debug
+
+
+/*
+ * ChangeLog
+ * $Log: Debug.java,v $
+ * Revision 1.7 2001/05/08 15:50:47 lord
+ * Spam suppression
+ *
+ * Revision 1.6 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/11/09 16:42:13 lord
+ * Package update
+ *
+ * Revision 1.4 2000/05/08 16:26:11 lord
+ * More informative when Debug instance is changed.
+ * Added getInstance method.
+ * Added horror of horrors, documentation
+ *
+ * Revision 1.3 2000/04/19 17:17:13 lord
+ * Changed main switch field to "debug" rather than "Debug"
+ *
+ * Revision 1.2 2000/03/09 18:02:47 lord
+ * Implemented default class
+ *
+ * Revision 1.1 2000/03/02 15:25:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/debug/DebugInterface.java b/src/uk/ac/man/bioinf/debug/DebugInterface.java
new file mode 100644
index 0000000..89c4cea
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/DebugInterface.java
@@ -0,0 +1,79 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+
+/**
+ * DebugInterface.java
+ *
+ *
+ * Created: Wed Mar 1 22:15:41 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DebugInterface.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface DebugInterface
+{
+ public void message( Object obj, String message );
+
+ public void message( Object obj, Object message );
+
+ public void message( Class cla, String message );
+
+ public void message( Class cla, Object message );
+
+ public void throwable( Object obj, Throwable th );
+
+ public void throwable( Class cla, Throwable th );
+
+ public void both( Object obj, String message, Throwable th );
+
+ public void both( Class cla, String message, Throwable th );
+
+ public void both( Object obj, Object message, Throwable th );
+
+ public void both( Class cla, Object message, Throwable th );
+
+}// DebugInterface
+
+
+/*
+ * ChangeLog
+ * $Log: DebugInterface.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/09 16:42:13 lord
+ * Package update
+ *
+ * Revision 1.1 2000/03/02 15:25:59 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/debug/DebugMultiplexer.java b/src/uk/ac/man/bioinf/debug/DebugMultiplexer.java
new file mode 100644
index 0000000..dc5236a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/DebugMultiplexer.java
@@ -0,0 +1,341 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+
+
+/**
+ * DebugMultiplexer.java
+ *
+ * This class can be used to multiplex other DebugInterface
+ * interfaces. It implements DebugInterface directly, rather than
+ * extending AbstractInterface, because I want to make no assumptions
+ * at all about the instances which it contains.
+ *
+ * This class has two relevant methods public methods to install and
+ * remove other DebugInterface instances. The first time install is called the
+ * multiplexer automatically installs itself as the primary
+ * DebugInterface instance. If all but one of its DebugInterface instances are removed
+ * from it, then it will replace itself as the primary interface with
+ * a DefaultDebug instance.
+ *
+ * If any of the Debug instances fail at any time in any of their
+ * methods, they will be removed. If Debug is true all of the others
+ * instances will be informed of this.
+ *
+ * Created: Sun May 7 20:49:33 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DebugMultiplexer.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DebugMultiplexer implements DebugInterface
+{
+ // store contents in array. We are probably not going to do a lot of
+ // adding and removing, but are going to do a lot of iterating, and
+ // this will save us loads of casts.
+ private static DebugInterface[] instArray;
+
+ private DebugMultiplexer()
+ {
+ //
+ }
+
+ /**
+ * Add a new Debug Interface instance. This method ensures that the
+ * Multiplexer is installed if it has not been so far. Note that
+ * this means the old debug instance is silently replaced and junked!
+ * @param deb
+ * @return
+ */
+ public static DebugInterface addDebugInstance( DebugInterface deb )
+ {
+ if( instArray == null || instArray.length == 0 ){
+ // small one element array
+ instArray = new DebugInterface[ 1 ];
+ instArray[ 0 ] = deb;
+ installDebugInstance();
+ }else{
+ // copy the old array and add the new at the end
+ DebugInterface[] newArray = new DebugInterface[ instArray.length + 1 ];
+ System.arraycopy( instArray, 0, newArray, 0, instArray.length );
+ newArray[ newArray.length - 1 ] = deb;
+ instArray = newArray;
+ }
+ if( Debug.debug )
+ Debug.message( DebugMultiplexer.class, "DEBUG: Multiplexer has added new instance " + deb );
+
+ return deb;
+ }
+
+ private static void installDebugInstance()
+ {
+ DebugInterface inst = new DebugMultiplexer();
+ Debug.setInstance( inst );
+ }
+
+
+ /**
+ * Remove a DebugInterface instance from the multiplexer.
+ * @param deb the interface to remove
+ * @return the interface removed. Null if the deb wasnt there
+ */
+ public static DebugInterface removeDebugInstance( DebugInterface deb )
+ {
+ DebugInterface old = deb;
+
+ int index = indexOf( deb );
+ if( index == -1 ){
+ return null;
+ }
+
+ // if its the last kill the array
+ if( instArray.length == 1 ){
+ DebugInterface last = instArray[ 0 ];
+ uninstallDebugInstance();
+ instArray = null;
+ return last;
+ }
+
+ // else remove the index
+ DebugInterface newInst[] = new DebugInterface
+ [ instArray.length - 1 ];
+ int numMoved = newInst.length - index;
+ System.arraycopy( instArray, 0, newInst, 0, index );
+ System.arraycopy( instArray, index + 1, newInst, index, numMoved );
+ instArray = newInst;
+
+ if( Debug.debug )
+ Debug.message( DebugMultiplexer.class,
+ "DEBUG: Have removed instance from multiplexer " + old );
+
+ return old;
+ }
+
+ private static int indexOf( DebugInterface deb )
+ {
+ if( instArray == null ) return -1;
+ for( int i = 0; i < instArray.length; i++ ){
+ if( deb == instArray[ i ] )
+ return i;
+ }
+ return -1;
+ }
+
+ private static void emergencyUninstall()
+ {
+ instArray = new DebugInterface[ 0 ];
+ Debug.setInstance( new DefaultDebug() );
+ Debug.message( DebugMultiplexer.class,
+ "DEBUG: PANIC! EMERGENCY! Uninstall of DebugMultiplexer!" );
+ }
+
+
+ private static void uninstallDebugInstance()
+ {
+ Debug.setInstance
+ ( instArray[ 0 ] );
+ }
+
+ private void handleDisaster( Throwable th )
+ {
+ emergencyUninstall();
+ if( Debug.debug )
+ Debug.throwable( DebugMultiplexer.class, th );
+ }
+
+ // the rest of the methods are all pretty much the same template,
+ // and I could not think of a better way of doing this...
+ public void message( Object obj, String message )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].message( obj, message );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable th ){
+ handleDisaster( th );
+ // "rethrow" the old message
+ Debug.message( obj, message );
+ }
+ }
+
+ public void message( Object obj, Object message )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].message( obj, message );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable th ){
+ handleDisaster( th );
+ // "rethrow" the old message
+ Debug.message( obj, message );
+ }
+ }
+
+ public void message( Class cla, String message )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].message( cla, message );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable th ){
+ handleDisaster( th );
+ // "rethrow" the old message
+ Debug.message( cla, message );
+ }
+ }
+
+
+ public void message( Class cla, Object message )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].message( cla, message );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable th ){
+ handleDisaster( th );
+ // "rethrow" the old message
+ Debug.message( cla, message );
+ }
+ }
+
+ public void throwable( Object obj, Throwable th )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].throwable( obj, th );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable tha ){
+ handleDisaster( tha );
+ // "rethrow" the old message
+ Debug.message( obj, th );
+ }
+ }
+
+
+ public void throwable( Class cla, Throwable th )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].throwable( cla, th );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable tha ){
+ handleDisaster( tha );
+ // "rethrow" the old message
+ Debug.message( cla, th );
+ }
+ }
+
+ public void both( Object obj, String message, Throwable th )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].both( obj, message, th );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable tha ){
+ handleDisaster( tha );
+ // "rethrow" old message
+ Debug.both( obj, message, th );
+ }
+ }
+
+ public void both( Class cla, String message, Throwable th )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].both( cla, message, th );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable tha ){
+ handleDisaster( tha );
+ // "rethrow" the old message
+ Debug.both( cla, message, th );
+ }
+ }
+
+ public void both( Object obj, Object message, Throwable th )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].both( obj, message, th );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable tha ){
+ handleDisaster( tha );
+ // "rethrow" the old message
+ Debug.both( obj, message, th );
+ }
+ }
+
+ public void both( Class cla, Object message, Throwable th )
+ {
+ int i = 0;
+ try{
+ for( i = 0; i < instArray.length; i++ ){
+ instArray[ i ].both( cla, message, th );
+ } //end for( i < instArray.length )
+ }
+ catch( Throwable tha ){
+ handleDisaster( tha );
+ // "rethrow" the old message
+ Debug.both( cla, message, th );
+ }
+ }
+} // DebugMultiplexer
+
+
+
+/*
+ * ChangeLog
+ * $Log: DebugMultiplexer.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.1 2000/05/08 16:22:57 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/debug/DefaultDebug.java b/src/uk/ac/man/bioinf/debug/DefaultDebug.java
new file mode 100644
index 0000000..fd328b6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/DefaultDebug.java
@@ -0,0 +1,77 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+
+
+/**
+ * DefaultDebug.java
+ *
+ * Simple Debug interface which prints things to screen
+ *
+ * Created: Thu Mar 9 17:57:34 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultDebug.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultDebug extends AbstractDebug
+{
+
+ public void message( Class cla, String message )
+ {
+ System.out.println( "Debug Message: " + message );
+ }
+
+ public void throwable( Class cla, Throwable th )
+ {
+ System.out.println( "Debug Throwable: " + th );
+ System.out.print( "Debug Stack: " );
+
+ th.printStackTrace();
+ }
+} // DefaultDebug
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultDebug.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/05/08 16:26:42 lord
+ * Now dumps stack also
+ *
+ * Revision 1.2 2000/04/20 14:04:38 lord
+ * Cosmetic changes to output
+ *
+ * Revision 1.1 2000/03/09 18:02:47 lord
+ * Implemented default class
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/debug/DefaultFileDebug.java b/src/uk/ac/man/bioinf/debug/DefaultFileDebug.java
new file mode 100644
index 0000000..4366a04
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/DefaultFileDebug.java
@@ -0,0 +1,85 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+import java.io.Writer;
+import java.io.File;
+import java.io.PrintWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+
+
+/**
+ * DefaultFileDebug.java
+ *
+ *
+ * Created: Sun May 7 23:46:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultFileDebug.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultFileDebug extends AbstractDebug
+{
+ private File file;
+ private PrintWriter writer;
+
+ public DefaultFileDebug( File file ) throws IOException
+ {
+ this.file = file;
+ writer = new PrintWriter( new FileWriter( file ) );
+ }
+
+ public void message( Class cla, String message )
+ {
+ writer.println( "Debug Message: " + message );
+ writer.flush();
+ }
+
+ public void throwable( Class cla, Throwable th )
+ {
+ writer.println( "Debug Throwable: " + th );
+ writer.println( "Debug Stack: " );
+
+ th.printStackTrace( writer );
+ writer.flush();
+ }
+} // DefaultFileDebug
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultFileDebug.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:22:57 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/debug/NullDebug.java b/src/uk/ac/man/bioinf/debug/NullDebug.java
new file mode 100644
index 0000000..ff8d08d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/debug/NullDebug.java
@@ -0,0 +1,67 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.debug; // Package name inserted by JPack
+
+
+/**
+ * NullDebug.java
+ *
+ * This class does nothing with debug methods. Very useful for
+ * clearing out spam quickly!
+ *
+ * Created: Tue May 16 12:42:54 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NullDebug.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class NullDebug extends AbstractDebug
+{
+ public void message( Class cla, String message )
+ {
+ }
+
+ public void throwable( Class cla, Throwable th )
+ {
+ }
+
+} // NullDebug
+
+
+
+/*
+ * ChangeLog
+ * $Log: NullDebug.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/18 17:08:21 lord
+ * Inital checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/ColorGenerator.java b/src/uk/ac/man/bioinf/gui/color/ColorGenerator.java
new file mode 100644
index 0000000..27ccc6f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ColorGenerator.java
@@ -0,0 +1,93 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+import java.awt.Color;
+
+/**
+ * ColorGenerator.java
+ *
+ * This class generates a stream of colours, cycling through all of
+ * the colours in the list until it has finished.
+ *
+ * Created: Wed May 24 09:54:25 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ColorGenerator.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ColorGenerator
+{
+
+ public static ColorGenerator getAllColorGenerator()
+ {
+ return new ColorGenerator();
+ }
+
+ public static ColorGenerator getLightColorGenerator()
+ {
+ return new ColorGenerator( ColorStore.lightColor );
+ }
+
+ private Color[] colors;
+ private int index = -1;
+
+ public ColorGenerator()
+ {
+ this( ColorStore.allColor );
+ }
+
+ public ColorGenerator( Color[] colors )
+ {
+ this.colors = colors;
+ }
+
+ public Color next()
+ {
+ if( ++index >= colors.length ){
+ index = 0;
+ }
+ return colors[ index ];
+ }
+} // ColorGenerator
+
+
+
+/*
+ * ChangeLog
+ * $Log: ColorGenerator.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/06/13 11:13:16 lord
+ * Moved storage code to ColorStore
+ *
+ * Revision 1.1 2000/05/24 15:38:15 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/ColorList.java b/src/uk/ac/man/bioinf/gui/color/ColorList.java
new file mode 100644
index 0000000..0895b0b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ColorList.java
@@ -0,0 +1,126 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+import java.awt.Color;
+
+
+/**
+ * ColorList.java
+ *
+ * This class is similar to ColorGenerator, except that instead of
+ * cycling through the colours it presents them as a list
+ *
+ * Created: Thu Jun 8 17:37:23 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ColorList.java,v 1.3 2002/03/08 14:52:36 lord Exp $
+ */
+
+public class ColorList
+{
+ public Color[] colors;
+
+ public ColorList()
+ {
+ this( ColorStore.allColor );
+ }
+
+ public ColorList( Color[] colors )
+ {
+ this.colors = colors;
+ }
+
+ public Color getColorAt( int index )
+ {
+ return colors[ index ];
+ }
+
+ public int length()
+ {
+ return colors.length;
+ }
+
+ private static ColorList allColList;
+ public static ColorList getAllColorList()
+ {
+ if( allColList == null )
+ new ColorList( ColorStore.allColor );
+ return allColList;
+ }
+
+ private static ColorList lightColList;
+ public static ColorList getLightColorList()
+ {
+ if( lightColList == null )
+ lightColList = new ColorList( ColorStore.lightColor );
+ return lightColList;
+ }
+
+ private static ColorList coldHotList;
+ public static ColorList getColdToHotColorList()
+ {
+ if( coldHotList == null )
+ coldHotList = new ColorList( ColorStore.coldToHot );
+ return coldHotList;
+ }
+
+ private static ColorList hotColdList;
+ public static ColorList getHotToColdColorList()
+ {
+ if( hotColdList == null )
+ hotColdList = new ColorList( ColorStore.hotToCold );
+ return hotColdList;
+ }
+
+ private static ColorList gray50;
+ public static ColorList getGray50List()
+ {
+ if( gray50 == null ){
+ gray50 = new ColorList( ColorStore.grayScale50 );
+ }
+ return gray50;
+ }
+
+} // ColorList
+
+
+
+/*
+ * ChangeLog
+ * $Log: ColorList.java,v $
+ * Revision 1.3 2002/03/08 14:52:36 lord
+ * Added another list
+ *
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/06/13 11:13:34 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/ColorMap.java b/src/uk/ac/man/bioinf/gui/color/ColorMap.java
new file mode 100644
index 0000000..858cd34
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ColorMap.java
@@ -0,0 +1,87 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+
+import java.awt.Color;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * ColorMap.java
+ *
+ * The interface to support color mapping of elements in a sequence
+ * alignment. NB: Objects of this type should be immutable.
+ *
+ * Created: Thu Mar 23 18:32:32 2000
+ *
+ * @author J Selley
+ * @version $Id: ColorMap.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface ColorMap
+{
+ /**
+ * Returns the Color at a specific position in the alignment. This
+ * method will do various things depending on the actual color map
+ * implemented.
+ *
+ * @param sa the sequence alignment
+ * @param elem the element
+ * @param point the location within the SA
+ * @return the color
+ */
+ public Color getColorAt(SequenceAlignment sa, Element elem, SequenceAlignmentPoint point);
+
+ /**
+ * Returns the name of this colour scheme.
+ *
+ * @return the name
+ */
+ public String getName();
+}// ColorMap
+
+
+/*
+ * ChangeLog
+ * $Log: ColorMap.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/09 16:42:13 lord
+ * Package update
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/04/11 18:29:06 jns
+ * o inial coding for color mapping.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/gui/color/ColorMapException.java b/src/uk/ac/man/bioinf/gui/color/ColorMapException.java
new file mode 100644
index 0000000..be37b5e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ColorMapException.java
@@ -0,0 +1,60 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+
+
+/**
+ * ColorMapException.java
+ *
+ *
+ * Created: Mon Apr 10 09:06:32 2000
+ *
+ * @author J Selley
+ * @version $Id: ColorMapException.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ColorMapException extends RuntimeException
+{
+ public ColorMapException(String message)
+ {
+ super(message);
+ }
+} // ColorMapException
+
+
+
+/*
+ * ChangeLog
+ * $Log: ColorMapException.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/11 18:29:41 jns
+ * o initial coding for color mapping.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/ColorStore.java b/src/uk/ac/man/bioinf/gui/color/ColorStore.java
new file mode 100644
index 0000000..a237b70
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ColorStore.java
@@ -0,0 +1,146 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+import java.awt.Color;
+
+
+/**
+ * ColorStore.java
+ *
+ * This is a static place holder of various lists of colours.
+ *
+ * Created: Thu Jun 8 17:39:09 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ColorStore.java,v 1.4 2002/03/08 15:04:45 lord Exp $
+ */
+
+public class ColorStore
+{
+ private ColorStore()
+ {
+ // no instances
+ }
+
+ static final Color[] allColor =
+ {
+ Color.white ,
+ Color.lightGray ,
+ Color.gray ,
+ Color.darkGray ,
+ Color.black ,
+ Color.red ,
+ Color.pink ,
+ Color.orange ,
+ Color.yellow ,
+ Color.green ,
+ Color.magenta ,
+ Color.cyan ,
+ Color.blue
+ };
+
+
+ static final Color[] lightColor =
+ {
+ Color.white ,
+ Color.red ,
+ Color.pink ,
+ Color.orange ,
+ Color.yellow ,
+ Color.green ,
+ Color.magenta ,
+ Color.cyan ,
+ Color.blue
+ };
+
+ static final Color[] coldToHot =
+ {
+ Color.blue ,
+ Color.cyan ,
+ Color.green ,
+ Color.yellow ,
+ Color.orange ,
+ Color.pink ,
+ Color.red
+ };
+
+ static final Color[] hotToCold =
+ {
+ Color.red ,
+ Color.pink ,
+ Color.orange ,
+ Color.yellow ,
+ Color.green ,
+ Color.cyan ,
+ Color.blue
+ };
+
+ static final Color[] grayScale5;
+ static final Color[] grayScale10;
+ static final Color[] grayScale50;
+
+ private static Color[] getGrayScale( int size )
+ {
+ Color[] array = new Color[ size ];
+
+ for( int i = 0; i < size; i++ ){
+ float j = 1.0f * i / (size - 1);
+ array[ i ] = new Color( j, j, j );
+ }
+
+ return array;
+ }
+
+ static
+ {
+ grayScale5 = getGrayScale( 5 );
+ grayScale10 = getGrayScale( 10 );
+ grayScale50 = getGrayScale( 50 );
+ }
+
+} // ColorStore
+
+
+
+/*
+ * ChangeLog
+ * $Log: ColorStore.java,v $
+ * Revision 1.4 2002/03/08 15:04:45 lord
+ * Removed debug statements
+ *
+ * Revision 1.3 2002/03/08 14:52:51 lord
+ * Added another list
+ *
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/06/13 11:13:34 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.java b/src/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.java
new file mode 100644
index 0000000..8b3d719
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/DoubleArrayColorMap.java
@@ -0,0 +1,106 @@
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by Jde-Package
+import java.awt.Color;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * DoubleArrayColorMap.java
+ *
+ * This class takes a series of doubles, a list of colours and a
+ * sequence alignment and turns them into a colour map.
+ *
+ * The list of doubles is a colour for every element in every
+ * sequence. Numbering starts at 0, and DOES NOT include gaps. Hence
+ * element 0,0 of the array is the first element of the first sequence
+ * where ever it starts.
+ *
+ * Created: Thu Jun 21 16:42:36 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: DoubleArrayColorMap.java,v 1.1 2002/03/08 14:53:36 lord Exp $
+ */
+
+public class DoubleArrayColorMap implements ColorMap
+{
+ private int[][] colourAtPosition;
+ private double[][] array;
+ private ColorList colors;
+
+ public DoubleArrayColorMap( double[][] array, ColorList colors )
+ {
+ this.array = array;
+ this.colors = colors;
+
+ // colourAtPosition = new int[ alignment.getNumberOfSequences() ][];
+
+// for( int i = 0; i < colourAtPostion.length;i++ ){
+// colorAtPosition[ i ] = new int [ alignment.getLength() ];
+// for( int j = 0; j < colorAtPosition[ i ].length; j++ ){
+
+// }
+// }
+ }
+
+ public Color getColorAt( SequenceAlignment sa, Element elem, SequenceAlignmentPoint point )
+ {
+ try{
+
+ if( elem == Gap.gap ) return Color.white;
+ if( elem == null ) return Color.white;
+
+ int yPosition = point.getY() - 1;
+ if( (point.getX() - sa.getInset( yPosition + 1 )) < 1 ){
+ return Color.white;
+ }
+
+ int xPosition = sa.getSequenceAt( yPosition + 1 ).getUngappedPositionOf
+ ( point.getX() - sa.getInset( yPosition + 1 ) ) - 1;
+
+ if( xPosition < 0 ){
+ return Color.white;
+ }
+
+ //System.out.println( "Requesting colour for " + yPosition + " " + xPosition );
+ return colors.getColorAt( (int)(array[ yPosition ][ xPosition ] * (colors.length() - 1 ) ) );
+ }
+
+ catch( ArrayIndexOutOfBoundsException aoofbe ){
+ System.out.println(aoofbe.getMessage());
+ return Color.green;
+ }
+
+ }
+
+
+ public String getName()
+ {
+ return "DoubleArrayColorMap";
+ }
+
+} // DoubleArrayColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: DoubleArrayColorMap.java,v $
+ * Revision 1.1 2002/03/08 14:53:36 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.java b/src/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.java
new file mode 100644
index 0000000..4290858
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/IndividualElementColorMap.java
@@ -0,0 +1,143 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.util.HashMap;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * IndividualElementColorMap.java
+ *
+ * Allows a direct mapping between an element and a color; thereby
+ * every element in a sequence type will have an associated color.
+ * NB: This class is <b>NOT</b> synchronized.
+ *
+ * Created: Thu Apr 6 13:13:24 2000
+ *
+ * @author J Selley
+ * @version $Id: IndividualElementColorMap.java,v 1.8 2001/07/06 11:52:51 lord Exp $
+ */
+
+/*
+ * Please excuse the spelling of color - it is so as not to confuse
+ * our counterparts on the other side of the atlantic, and to keep
+ * with the spelling chosen for use in the Java API.
+ */
+
+public class IndividualElementColorMap implements ColorMap
+{
+ private String name;
+ private HashMap mapping = new HashMap(); // the mapping of elements to colors
+
+ public IndividualElementColorMap(String name,
+ Element[] elements,
+ Color[] colors)
+ {
+ this.name = name;
+ if (elements.length != colors.length)
+ throw new ColorMapException("The number of elements and colors supplied " +
+ "are not the same");
+ for (int i = 0; i < elements.length; i++) {
+ mapping.put(elements[i], colors[i]);
+ }
+ }
+
+ /**
+ * Returns the color for an element at a specific position in the
+ * alignment. [from ColorMap] NB: In this case, this simply
+ * identifies the element and returns the color for that element.
+ *
+ * @param sa the sequence alignment
+ * @param element the element from the position in the SA
+ * @param point the position in the SA
+ * @return the color of the element
+ */
+ public Color getColorAt
+ (SequenceAlignment sa, Element element, SequenceAlignmentPoint point)
+ {
+ if( element == null ) return null;
+
+ /*
+ int trueElementPosition = point.getX() - sa.getInset(point.getY());
+ if ((trueElementPosition > 0) &&
+ (trueElementPosition < ((DefaultGappedSequence)
+ sa.getSequenceAt(point.getY())).getLength()) &&
+ (element != ((DefaultGappedSequence)sa.getSequenceAt(point.getY())).
+ getGappedElementAt(trueElementPosition)))
+ throw new ColorMapException("The supplied element and the element at " +
+ "the given point do not match");
+ */
+ return (Color)mapping.get(element);
+ }
+
+ /**
+ * Returns the name of this color map.
+ *
+ * @return the color map name
+ */
+ public String getName()
+ {
+ return this.name;
+ }
+} // IndividualElementColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: IndividualElementColorMap.java,v $
+ * Revision 1.8 2001/07/06 11:52:51 lord
+ * Changed error message.
+ *
+ * Revision 1.7 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.5 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.4 2000/05/18 17:07:43 lord
+ * Removed error checking as its probably not necessary.
+ *
+ * Revision 1.3 2000/05/08 16:29:08 lord
+ * Checks for null element which saves unnecessary hash lookup
+ *
+ * Revision 1.2 2000/04/12 13:37:15 jns
+ * o added in checking for insets and end of sequence to prevent
+ * the throwing of the exception.
+ *
+ * Revision 1.1 2000/04/11 18:30:09 jns
+ * o initial coding for color mapping.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.java b/src/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.java
new file mode 100644
index 0000000..22598dd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/PercentIDVarianceColorMap.java
@@ -0,0 +1,145 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+
+import java.awt.Color;
+import uk.ac.man.bioinf.analysis.misc.PercentageIDCalculator;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * PercentIDVarianceColorMap.java
+ *
+ * Calculates a colour scheme
+ *
+ * Created: Fri Jun 9 16:03:46 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: PercentIDVarianceColorMap.java,v 1.10 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class PercentIDVarianceColorMap implements ThreadableColorMap
+{
+ public static final String NAME = "Percentage ID variance Color Map";
+ private ColorList colors;
+ private PercentageIDCalculator calculator;
+ private int[] colorAtColumn;
+
+ public PercentIDVarianceColorMap( PercentageIDCalculator calculator )
+ {
+ this( calculator, ColorList.getHotToColdColorList() );
+ }
+
+ public PercentIDVarianceColorMap( PercentageIDCalculator calculator, ColorList lowToHighColours )
+ {
+ this.calculator = calculator;
+ this.colors = lowToHighColours;
+
+ calculate();
+ }
+
+ public Color getColorAt(SequenceAlignment sa, Element elem, SequenceAlignmentPoint point)
+ {
+ if( elem == null || elem == Gap.GAP ) return null;
+ try{
+ return colors.getColorAt( colorAtColumn[ point.getX() - 1 ] );
+ }
+ catch( ArrayIndexOutOfBoundsException iob ){
+ System.out.println( "Iob exception at col " + point.getX() );
+ }
+ return null;
+ }
+
+ public String getName()
+ {
+ return NAME;
+ }
+
+ public void calculate()
+ {
+ double[] variance = calculator.getVariance();
+
+ int[] colorAtColumn = new int[ variance.length ];
+
+ for( int i = 0; i < colorAtColumn.length; i++ ){
+ colorAtColumn[ i ] = (int)(variance[ i ] * (colors.length() - 1 ) );
+ }
+
+ this.colorAtColumn = colorAtColumn;
+ }
+} // PercentIDVarianceColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: PercentIDVarianceColorMap.java,v $
+ * Revision 1.10 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.9 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.8 2000/12/05 15:20:41 lord
+ * Changes to ensure that the class is in a consistent state even whilst
+ * the calculate method is being called.
+ *
+ * Revision 1.7 2000/09/25 16:36:44 lord
+ * Inserted null element check
+ *
+ * Revision 1.6 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.5 2000/07/26 13:36:59 lord
+ * Several changes. Mostly though pass in the PercentageIDCalculator in
+ * the command line
+ *
+ * Revision 1.4 2000/07/18 11:08:25 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/06/27 15:59:15 lord
+ * Now uses PercentageIDCalculator class so that I can rationalise the
+ * code in here with the PercentageIDConsensus class
+ *
+ * Revision 1.2 2000/06/19 14:31:23 lord
+ * Have changed implementation to use integers instead
+ *
+ * Revision 1.1 2000/06/13 11:13:34 lord
+ * Initial checkin
+ *
+ */
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/gui/color/SingleColorMap.java b/src/uk/ac/man/bioinf/gui/color/SingleColorMap.java
new file mode 100644
index 0000000..9550ce4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/SingleColorMap.java
@@ -0,0 +1,94 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+
+import java.awt.Color;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * SingleColorMap.java
+ *
+ * This class is designed to return one color, regardless of the
+ * element being displayed. Thus, this is able to provide no color
+ * scheme, by being set to the background color at run time.
+ *
+ * Created: Tue Apr 11 17:42:19 2000
+ *
+ * @author J Selley
+ * @version $Id: SingleColorMap.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class SingleColorMap implements ColorMap
+{
+ private String name;
+ private Color color;
+
+ public SingleColorMap( Color color )
+ {
+ this( color, "SingleColorMap" );
+ }
+
+ public SingleColorMap( Color color, String name )
+ {
+ this.name = name;
+ this.color = color;
+ }
+
+ public Color getColorAt
+ (SequenceAlignment sa, Element element, SequenceAlignmentPoint point)
+ {
+ return this.color;
+ }
+
+ public String getName()
+ {
+ return this.name;
+ }
+} // SingleColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: SingleColorMap.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/02/19 17:40:32 lord
+ * Now takes a colour in the constructor
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/04/11 18:30:34 jns
+ * o initial coding for color mapping.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/ThreadableColorMap.java b/src/uk/ac/man/bioinf/gui/color/ThreadableColorMap.java
new file mode 100644
index 0000000..9bd762f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ThreadableColorMap.java
@@ -0,0 +1,64 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+
+
+/**
+ * ThreadableColorMap.java
+ *
+ * Defines a color map that can perform any necessary calculations to
+ * in a thread safe manner. The class is not required to perform the
+ * threading, but it is required to perform the calculation in a
+ * thread safe way. In other words the getColorAt() method should
+ * function safely even whilst calculate method is being called.
+ *
+ * Created: Fri Dec 1 14:45:34 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ThreadableColorMap.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface ThreadableColorMap extends ColorMap
+{
+ public void calculate();
+
+} // ThreadableColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: ThreadableColorMap.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/05 15:20:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/color/ThreadedColorMap.java b/src/uk/ac/man/bioinf/gui/color/ThreadedColorMap.java
new file mode 100644
index 0000000..7a7fed5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/color/ThreadedColorMap.java
@@ -0,0 +1,175 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.color; // Package name inserted by JPack
+import java.awt.Color;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import uk.ac.man.bioinf.apps.invoker.AnonInvoker;
+import uk.ac.man.bioinf.apps.invoker.InvokerInternalQueue;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * ThreadedColorMap.java
+ *
+ * This class implements the threaded functionality for ColorMap. You
+ * can use this class to wrap up any other ThreadableColorMap and it
+ * will take care of the out thread calculation.
+ *
+ * This class it should be noted is immutable in the sense that the
+ * SequenceAlignment it set in the constructor, and you can not change
+ * this, so you will need to create a new object.
+ *
+ *
+ * Created: Fri Dec 1 14:58:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ThreadedColorMap.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ThreadedColorMap implements ColorMap, SequenceListener, AlignmentListener, PropertyChangeListener
+{
+ public static final String NAME = "Threaded Color Map";
+
+ private InvokerInternalQueue queue;
+ private SequenceAlignment alignment;
+ private ThreadableColorMap map;
+ private JAlignmentViewer viewer;
+
+ public ThreadedColorMap( JAlignmentViewer viewer, SequenceAlignment alignment, ThreadableColorMap map )
+ {
+ this( viewer, alignment, map, new InvokerInternalQueue() );
+ }
+
+ public ThreadedColorMap( JAlignmentViewer viewer, SequenceAlignment alignment,
+ ThreadableColorMap map, InvokerInternalQueue queue )
+ {
+ this.alignment = alignment;
+ this.queue = queue;
+ this.map = map;
+ this.viewer = viewer;
+
+ viewer.addPropertyChangeListener( this );
+
+ alignment.addAlignmentListener( this );
+ alignment.addSequenceListener( this );
+ }
+
+ public Color getColorAt( SequenceAlignment alignment, Element element,
+ SequenceAlignmentPoint point )
+ {
+ return map.getColorAt( alignment, element, point );
+ }
+
+ protected void validate()
+ {
+
+ // we want to do the calculation out of the event thread, and then
+ // fire change events back in it...
+ queue.makeEmpty();
+ queue.enqueue
+ ( new AnonInvoker(){
+ long start;
+
+ public Object slow()
+ {
+ ThreadedColorMap.this.map.calculate();
+ return null;
+ }
+
+ public void doRun()
+ {
+ ThreadedColorMap.this.viewer.repaint();
+ }
+ });
+ }
+
+ public void propertyChange( PropertyChangeEvent event )
+ {
+ if( event.getPropertyName().equals( "colorMap" )
+ && event.getSource() == viewer
+ && event.getOldValue() == this ){
+ destroy();
+ }
+ }
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ validate();
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ validate();
+ }
+
+ public String getName()
+ {
+ return ThreadedColorMap.NAME;
+ }
+
+ public String getInternalThreadedColorMap()
+ {
+ return map.getName();
+ }
+
+ public void destroy()
+ {
+ queue.destroy();
+ queue = null;
+ alignment.removeSequenceListener( this );
+ alignment.removeAlignmentListener( this );
+ }
+} // ThreadedColorMap
+
+
+
+/*
+ * ChangeLog
+ * $Log: ThreadedColorMap.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/13 16:32:10 lord
+ * Cosmetic and debug statement removal
+ *
+ * Revision 1.2 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/12/05 15:20:59 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/misc/ChunkyListModel.java b/src/uk/ac/man/bioinf/gui/misc/ChunkyListModel.java
new file mode 100644
index 0000000..979ee02
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/misc/ChunkyListModel.java
@@ -0,0 +1,362 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex as a reseach fellow, on a
+ * project funded by the Birth Defects Foundation.
+ *
+ * The initial code base is copyright by the University of Middlesex,
+ * or the Birth Defects Foundation, or even possibly by me.
+ * Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+package uk.ac.man.bioinf.gui.misc; // Package name inserted by JPack
+
+import java.util.Collection;
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
+import javax.swing.AbstractListModel;
+
+/**
+ * ChunkyListModel.java
+ *
+ * This is a small extension to the list model class. It allows the addition
+ * of several elements at once, with only one fireIntervalAdded event occuring.
+ * The reason for this is essentially performance. The DefaultListModel appears
+ * to cause a huge amount of repainting whilst it is being loaded with data, which
+ * means that it gets a lot slower to add elements when they already are. Whilst there
+ * are probably better ways to solve this problem, the simplest would appear to be
+ * add the elements in chunks.
+ *
+ * Since I have written this code I have found various other ways
+ * around the repaint problem. However this code is still pretty
+ * useful because its got some nice convenience methods for adding and
+ * removing many elements at once.
+ *
+ * The class name is still pretty terrible though.
+ *
+ * <P>
+ * Created: Tue Nov 17 13:43:56 1998
+ * <P>
+ * Compliant: 1.0
+ *
+ * @author Phillip Lord
+ * @version $Id: ChunkyListModel.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+public class ChunkyListModel extends AbstractListModel
+{
+ private Vector delegate = new Vector();
+
+ public ChunkyListModel()
+ {
+ super();
+ }
+
+
+ /**
+ * This method takes a collection, adds all the elements,
+ * then fires an event. This method isnt thread safe, call
+ * from the event thread only
+ * @param c the collection to be added
+ */
+ public void addAll( Collection collection )
+ {
+ addAll( collection.toArray() );
+ }
+
+ /**
+ * Add all the elements of this array to the list model
+ * @param object the array
+ */
+ public void addAll( Object[] object )
+ {
+ //The start and stop indexes
+ int startIndex = delegate.size();
+ int stopIndex = startIndex + object.length;
+
+ //Add them all
+ for ( int i = 0; i < object.length; i++ ){
+ delegate.addElement( object[ i ] );
+ }
+
+ //Inform everything its happened
+ fireIntervalAdded( this, startIndex, stopIndex );
+ }
+
+ /**
+ * Add all the elements of this vector to the list model
+ * @param vector the vector
+ */
+ public void addAll( Vector vector )
+ {
+ addAll( vector.toArray() );
+ }
+
+ public List toList()
+ {
+ return delegate;
+ }
+
+ Collection toCollection()
+ {
+ return delegate;
+ }
+
+ Vector toVector()
+ {
+ return delegate;
+ }
+
+ /**
+ * Removes all the elements of this array from the list modely
+ * @param object the array
+ */
+ public void removeAll( Object[] object )
+ {
+ for ( int i = 0; i < object.length; i ++ ){
+ removeElement( object[ i ] );
+ }
+ fireIntervalRemoved( this, 0, object.length );
+ }
+
+ public void removeAll( Vector vector )
+ {
+ removeAll( vector.toArray() );
+ }
+
+ public void removeAll( Collection collection )
+ {
+ removeAll( collection.toArray() );
+ }
+
+
+
+ /**
+ * Everything that follows this is just a straight copy from
+ * the default list model
+ * @return the size
+ */
+ public int getSize() {
+ return delegate.size();
+ }
+
+ public Object getElementAt(int index) {
+ return delegate.elementAt(index);
+ }
+
+ public void copyInto(Object anArray[]) {
+ delegate.copyInto(anArray);
+ }
+
+ public void trimToSize() {
+ delegate.trimToSize();
+ }
+
+ public void ensureCapacity(int minCapacity) {
+ delegate.ensureCapacity(minCapacity);
+ }
+
+ public void setSize(int newSize) {
+ int oldSize = delegate.size();
+ delegate.setSize(newSize);
+ if (oldSize > newSize) {
+ fireIntervalRemoved(this, newSize, oldSize-1);
+ }
+ else if (oldSize < newSize) {
+ fireIntervalAdded(this, oldSize, newSize-1);
+ }
+ }
+
+ public int capacity() {
+ return delegate.capacity();
+ }
+
+ public int size() {
+ return delegate.size();
+ }
+
+ public boolean isEmpty() {
+ return delegate.isEmpty();
+ }
+
+ public Enumeration elements() {
+ return delegate.elements();
+ }
+
+ public boolean contains(Object elem) {
+ return delegate.contains(elem);
+ }
+
+ public int indexOf(Object elem) {
+ return delegate.indexOf(elem);
+ }
+
+ public int indexOf(Object elem, int index) {
+ return delegate.indexOf(elem, index);
+ }
+
+ public int lastIndexOf(Object elem) {
+ return delegate.lastIndexOf(elem);
+ }
+
+ public int lastIndexOf(Object elem, int index) {
+ return delegate.lastIndexOf(elem, index);
+ }
+
+ public Object elementAt(int index) {
+ return delegate.elementAt(index);
+ }
+
+ public Object firstElement() {
+ return delegate.firstElement();
+ }
+
+ public Object lastElement() {
+ return delegate.lastElement();
+ }
+
+ public void setElementAt(Object obj, int index) {
+ delegate.setElementAt(obj, index);
+ fireContentsChanged(this, index, index);
+ }
+
+ public void removeElementAt(int index) {
+ delegate.removeElementAt(index);
+ fireIntervalRemoved(this, index, index);
+ }
+
+ public void insertElementAt(Object obj, int index) {
+ delegate.insertElementAt(obj, index);
+ fireIntervalAdded(this, index, index);
+ }
+
+ public void addElement(Object obj) {
+ int index = delegate.size();
+ delegate.addElement(obj);
+ fireIntervalAdded(this, index, index);
+ }
+
+ public boolean removeElement(Object obj) {
+ int index = indexOf(obj);
+ boolean rv = delegate.removeElement(obj);
+ if (index > 0) {
+ fireIntervalRemoved(this, index, index);
+ }
+ return rv;
+ }
+
+
+ public void removeAllElements() {
+ int index1 = delegate.size()-1;
+ delegate.removeAllElements();
+ if (index1 >= 0) {
+ fireIntervalRemoved(this, 0, index1);
+ }
+ }
+
+
+ public String toString() {
+ return delegate.toString();
+ }
+
+ /* The remaining methods are included for compatibility with the
+ * JDK1.2 Vector class.
+ */
+
+ public Object[] toArray() {
+ Object[] rv = new Object[delegate.size()];
+ delegate.copyInto(rv);
+ return rv;
+ }
+
+ public Object get(int index) {
+ return delegate.elementAt(index);
+ }
+
+ public Object set(int index, Object element) {
+ Object rv = delegate.elementAt(index);
+ delegate.setElementAt(element, index);
+ fireContentsChanged(this, index, index);
+ return rv;
+ }
+
+ public void add(int index, Object element) {
+ delegate.insertElementAt(element, index);
+ fireIntervalAdded(this, index, index);
+ }
+
+ public Object remove(int index) {
+ Object rv = delegate.elementAt(index);
+ delegate.removeElementAt(index);
+ fireIntervalRemoved(this, index, index);
+ return rv;
+ }
+
+ public void clear() {
+ int index1 = delegate.size()-1;
+ delegate.removeAllElements();
+ if (index1 >= 0) {
+ fireIntervalRemoved(this, 0, index1);
+ }
+ }
+
+ public void removeRange(int fromIndex, int toIndex) {
+ for(int i = toIndex; i >= fromIndex; i--) {
+ delegate.removeElementAt(i);
+ }
+ fireIntervalRemoved(this, fromIndex, toIndex);
+ }
+
+
+} // ChunkyListModel
+
+
+
+/*
+ * ChangeLog
+ * $Log: ChunkyListModel.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/10/11 15:41:09 lord
+ * import sorting
+ *
+ * Revision 1.1 2000/06/05 14:21:25 lord
+ * Initial checkin in bioinf package
+ *
+ * Revision 1.3 1999/10/14 14:00:52 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.3 1999-10-12 14:47:31+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\editor\gui\ChunkyListModel.java,v').
+ *
+ * Revision 1.3 1999-10-04 16:22:21+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\editor\gui\ChunkyListModel.java,v').
+ *
+ * Revision 1.2 1999-05-17 12:37:20+01 phillip2
+ * Removed * from imports
+ *
+ * Revision 1.1 1999-02-02 16:04:00+00 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.java b/src/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.java
new file mode 100644
index 0000000..c617297
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/misc/SwappingListBasicUI.java
@@ -0,0 +1,145 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.misc; // Package name inserted by JPack
+import java.awt.event.MouseEvent;
+import javax.swing.DefaultListModel;
+import javax.swing.JList;
+import javax.swing.SwingUtilities;
+import javax.swing.event.MouseInputListener;
+import javax.swing.plaf.basic.BasicListUI;
+
+
+/**
+ * SwappingListBasicUI.java
+ *
+ * This class enables dragging of list items around something like
+ * XMMS's playlist.
+ * Because it has to modify the list it must perform a dodgy cast, to
+ * some form of modifiable ListModel. In this case it assumes that the
+ * list extends DefaultListModel. (PENDING:- PL) I should include some
+ * checking for this when ever the UI is associated with a JList or
+ * whenever the ListModel is changed, which would give me fail fast
+ * behaviour.
+ *
+ * Created: Tue Oct 3 18:40:07 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SwappingListBasicUI.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class SwappingListBasicUI extends BasicListUI
+{
+ protected MouseInputListener createMouseInputListener()
+ {
+ return new SwappingMouseInputHandler();
+ }
+
+ protected int convertYToRow( int y )
+ {
+ return super.convertYToRow( y );
+ }
+
+ protected JList getJList()
+ {
+ return list;
+ }
+
+ public class SwappingMouseInputHandler extends MouseInputHandler
+ {
+ private int indexOfElementBeingDragged = -1;
+
+ public void mousePressed( MouseEvent event )
+ {
+ // call the super class to get the selection stuff all working
+ // correctly.
+ super.mousePressed( event );
+
+ if( SwingUtilities.isLeftMouseButton( event ) ){
+ // and keep a record of the value that we first pressed on so
+ // that we can drag it.
+ int row = convertYToRow( event.getY() );
+ if( row != -1 ){
+ indexOfElementBeingDragged = row;
+ }
+ }
+ else{
+ // clear the drag
+ indexOfElementBeingDragged = -1;
+ }
+ }
+
+ public void mouseDragged( MouseEvent e )
+ {
+ if( SwingUtilities.isLeftMouseButton( e ) ){
+ int row = convertYToRow( e.getY() );
+
+ if( row != -1 && row != indexOfElementBeingDragged ){
+ int max = Math.max( row,indexOfElementBeingDragged );
+ int min = Math.min( row, indexOfElementBeingDragged );
+
+ swap( max, min );
+
+ // now remember where the element being dragged is
+ indexOfElementBeingDragged = row;
+ }
+ }
+ }
+
+ protected void swap( int max, int min )
+ {
+ JList list = getJList();
+
+ // here is the dodgy cast
+ DefaultListModel model = (DefaultListModel)list.getModel();
+
+ // this lots just swaps the stuff over
+ Object upper = model.remove( max );
+ Object lower = model.getElementAt( min );
+ model.insertElementAt( lower, max );
+ model.remove( min );
+ model.insertElementAt( upper, min );
+ }
+ }
+} // SwappingListBasicUI
+
+
+
+/*
+ * ChangeLog
+ * $Log: SwappingListBasicUI.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/10/12 11:30:14 lord
+ * Changes getJlist from private to protected
+ *
+ * Revision 1.1 2000/10/11 15:35:03 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.java b/src/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.java
new file mode 100644
index 0000000..5c2251a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/optionable/OptionableJFrame.java
@@ -0,0 +1,288 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software is copyright by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ */
+
+package uk.ac.man.bioinf.gui.optionable; // Package name inserted by JPack
+import java.awt.Dimension;
+import java.awt.Point;
+import java.util.HashMap;
+import javax.swing.JFrame;
+import javax.swing.JInternalFrame;
+import uk.ac.man.bioinf.apps.optionable.NullOptionHandler;
+import uk.ac.man.bioinf.apps.optionable.OptionHandler;
+import uk.ac.man.bioinf.apps.optionable.Optionable;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.apps.optionable.OptionableStateException;
+
+/**
+ * OptionableJFrame.java
+ *
+ *
+ * Created: Fri May 07 16:45:36 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: OptionableJFrame.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class OptionableJFrame extends JFrame
+ implements Optionable
+{
+ private String optionableName;
+
+ private OptionHandler optionHandler;
+ private boolean sizeSetAsOption = false;
+ private boolean locationSetAsOption = false;
+ private boolean haveOptioned = false;
+
+ public OptionableJFrame( String optionableName )
+ {
+ this( optionableName, "" );
+ }
+
+ /**
+ * An internal frame with a title
+ * @param title
+ */
+ public OptionableJFrame( String optionableName, String title )
+ {
+ this( optionableName, title, false );
+ }
+
+ /**
+ * No title. However if the param is true this class will not register
+ * its optionable status until explicitly told, rather than in the constructor.
+ * Subclasses which have their own options should use this option if they need
+ * to complete their own setOptions before their constructor is complete.
+ * @param delayOptionable delay setting options until explicitly told
+ * @see #forceOptionable
+ */
+ public OptionableJFrame( String optionableName, boolean delayOptionable )
+ {
+ this( optionableName, "", delayOptionable );
+ }
+
+ public OptionableJFrame( String optionableName, String title,
+ boolean delayOptionable )
+ {
+ this( optionableName, title, delayOptionable, null );
+ }
+
+ /**
+ * A title and the ability to delay the registering of the optionable
+ * status
+ * @param optionableName the name used to identify this Frame to the
+ * optionable library.
+ * @param title the title
+ * @param delayOptionable delay setting optionable status
+ */
+ public OptionableJFrame( String optionableName, String title,
+ boolean delayOptionable, OptionHandler handler )
+ {
+ super( title );
+ this.optionableName = optionableName;
+ this.optionHandler = optionHandler;
+
+ if( !delayOptionable ){
+ forceOptionable();
+ }
+ }
+
+
+ public void setOptions() throws OptionableStateException
+ {
+ if( haveOptioned ){
+ throw new OptionableStateException( "Have already set the optionable status of this frame" );
+ }
+ forceOptionable();
+ }
+
+ /**
+ * Force the setting the optionable status now. This method
+ * excepts if it is called more than once per object, or if a constructor without
+ * the delayOptionable parameter has NOT been used
+ * @throws RuntimeException if called illegally
+ */
+ protected void forceOptionable()
+ {
+ if( haveOptioned )
+ throw new RuntimeException( "Have already set the optionable status of this frame" );
+ getOptionHandler().addOptionable( this );
+ haveOptioned = true;
+ }
+
+ /**
+ * This sets the size of the frame, only if it hasnt been set as an option. This
+ * allows a default size to be set outside the constructor. The setSize() method
+ * sets the size regardless of whether it has been set previously
+ * @param x the width
+ * @param y the height
+ */
+ public void setDefaultSize( int x, int y )
+ {
+ //Set the size only if it hasnt been set by an option.
+ if( !sizeSetAsOption ){
+ super.setSize( x, y );
+ }
+ }
+
+ /**
+ * Pretty much the same as setDefaultSize
+ * @see #setDefaultSize
+ * @param x the x location
+ * @param y the y location
+ */
+ public void setDefaultLocation( int x, int y )
+ {
+ if( !locationSetAsOption ){
+ super.setLocation( x, y );
+ }
+ }
+
+ /**
+ * Pack the frame if the size hasnt been sized by its options
+ */
+ public void defaultPack()
+ {
+ if( !locationSetAsOption ){
+ super.pack();
+ }
+ }
+
+ /**
+ * An implementation of the Optionable interface. Subclasses overriding this method
+ * should call super.getOptions. Also the constructor documentation and the delayOptionable
+ * parameter should be considered.
+ * @return the options
+ */
+ public Object getOptions()
+ {
+ HashMap options = new HashMap();
+ //Place the options regarding size and location into a hashmap.
+ options.put( "frameSize", getSize() );
+ options.put( "frameLocation", getLocation() );
+ return options;
+ }
+
+ /**
+ * Implementation of the Optionable Interface.
+ * @see getOptions
+ * @param param1
+ */
+ public void setOptions(Object param1)
+ {
+ try{
+ if ( param1 == null ) return;
+ HashMap options = (HashMap)param1;
+ //Size and location
+ setSize( new Dimension( 300, 300 ) );
+ setSize( (Dimension)options.get( "frameSize" ) );
+ sizeSetAsOption = true;
+ setLocation( (Point)options.get( "frameLocation" ) );
+ locationSetAsOption = true;
+ }
+ catch( NullPointerException ex ){
+ //We can just ignore this. It should only occur when the options have
+ //not be set for the first time
+ if( Debug.debug ){
+ System.out.println( "Null pointer exception occuring in OptionableInternalFrame, setOptions" );
+ ex.printStackTrace();
+ }
+ }
+ catch( ClassCastException ex ){
+ //This should only occur during development
+ if( Debug.debug ){
+ System.out.println( "ClassCastException occuring in OptionableInternalFrame, setOptions" );
+ }
+ }
+ }
+
+ /**
+ * Implementation of the OptionableInterface
+ * @param OptionHandler the optionhandler
+ */
+ public void setOptionHandler( OptionHandler optionHandler )
+ {
+ this.optionHandler = optionHandler;
+ }
+
+ /**
+ * Implementation of the Optionable interface
+ * @return the option handler
+ */
+ public OptionHandler getOptionHandler()
+ {
+ if( optionHandler == null ){
+ return getDefaultOptionHandler();
+ }
+ else{
+ return optionHandler;
+ }
+ }
+
+ /**
+ * Subclasses must provide this, either on a class or instance basis
+ * @return the Option group name
+ */
+ public String getOptionGroupName()
+ {
+ return optionableName;
+ }
+
+ private static OptionHandler defaultOptionHandler;
+ public static void setDefaultOptionHandler( OptionHandler optionHandler )
+ {
+ defaultOptionHandler = optionHandler;
+ }
+
+ public static OptionHandler getDefaultOptionHandler()
+ {
+ if( defaultOptionHandler == null ){
+ return NullOptionHandler.getInstance();
+ }
+ return defaultOptionHandler;
+ }
+} // OptionableJFrame
+
+
+
+/*
+ * ChangeLog
+ * $Log: OptionableJFrame.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:42:53 lord
+ * Initial checkin
+ *
+ * Revision 1.3 1999/10/14 14:00:52 phillip2
+ * Changed packages and a few other bits and bobs
+ *
+ * Revision 1.3 1999-10-12 14:47:46+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\editor\gui\OptionableJFrame.java,v').
+ *
+ * Revision 1.3 1999-10-04 16:24:19+01 phillip2
+ * Outdated (renamed to 'D:\Home\rcs\D\Home\java\sources\photofit\editor\gui\OptionableJFrame.java,v').
+ *
+ * Revision 1.2 1999-10-01 16:56:20+01 phillip2
+ * Added import statements due to changed package structure
+ *
+ * Revision 1.1 1999-05-14 14:39:05+01 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.java b/src/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.java
new file mode 100644
index 0000000..39b7918
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/optionable/OptionableJSplitPane.java
@@ -0,0 +1,160 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.optionable; // Package name inserted by JPack
+import javax.swing.JSplitPane;
+import uk.ac.man.bioinf.apps.optionable.OptionHandler;
+import uk.ac.man.bioinf.apps.optionable.OptionableStateException;
+import uk.ac.man.bioinf.apps.optionable.NullOptionHandler;
+import uk.ac.man.bioinf.apps.optionable.Optionable;
+
+
+/**
+ * OptionableJSplitPane.java
+ *
+ * Stores the divider location as an option
+ *
+ * Created: Fri Feb 2 17:55:18 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: OptionableJSplitPane.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class OptionableJSplitPane extends JSplitPane implements Optionable
+{
+ private String optionableName;
+
+ private OptionHandler optionHandler;
+ private boolean locationSetAsOption = false;
+ private boolean haveOptioned;
+
+ public OptionableJSplitPane( String optionableName )
+ {
+ super();
+ this.optionableName = optionableName;
+ forceOptionable();
+ }
+
+ public OptionableJSplitPane( String optionableName, int orientation )
+ {
+ super( orientation );
+ this.optionableName = optionableName;
+ forceOptionable();
+ }
+
+ public void setDefaultDividerLocation( int location )
+ {
+ if( !locationSetAsOption ){
+ super.setDividerLocation( location );
+ }
+ }
+
+ public void setOptions() throws OptionableStateException
+ {
+ if( haveOptioned ){
+ throw new OptionableStateException( "Have already set the optionable status of this frame" );
+ }
+ forceOptionable();
+ }
+
+ protected void forceOptionable()
+ {
+ if( haveOptioned )
+ throw new RuntimeException( "Have already set the optionable status of this frame" );
+ getOptionHandler().addOptionable( this );
+ haveOptioned = true;
+ }
+
+ public Object getOptions()
+ {
+ return new Integer( getDividerLocation() );
+ }
+
+ public void setOptions( Object options )
+ {
+ try{
+ if( options != null ){
+ setDividerLocation( ((Integer)options).intValue() );
+ locationSetAsOption = true;
+ }
+ }
+ catch( ClassCastException cce ){
+ // should only occur during development or version change
+ }
+ }
+
+ public void setOptionHandler( OptionHandler optionHandler )
+ {
+ this.optionHandler = optionHandler;
+ }
+
+ public OptionHandler getOptionHandler()
+ {
+ if( optionHandler == null ){
+ return getDefaultOptionHandler();
+ }
+ else{
+ return optionHandler;
+ }
+ }
+
+ public String getOptionGroupName()
+ {
+ return optionableName;
+ }
+
+ private static OptionHandler defaultOptionHandler;
+ public static void setDefaultOptionHandler( OptionHandler optionHandler )
+ {
+ defaultOptionHandler = optionHandler;
+ }
+
+ public static OptionHandler getDefaultOptionHandler()
+ {
+ if( defaultOptionHandler == null ){
+ return NullOptionHandler.getInstance();
+ }
+ return defaultOptionHandler;
+ }
+} // OptionableJSplitPane
+
+
+
+/*
+ * ChangeLog
+ * $Log: OptionableJSplitPane.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/03/12 16:48:48 lord
+ * New constructors added
+ *
+ * Revision 1.1 2001/02/19 17:42:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/util/ApplicationFrame.java b/src/uk/ac/man/bioinf/gui/util/ApplicationFrame.java
new file mode 100644
index 0000000..b9832f5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/ApplicationFrame.java
@@ -0,0 +1,377 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util;
+import uk.ac.man.bioinf.util.*;
+import javax.swing.*;
+import java.util.*;
+import java.io.IOException;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.awt.Dimension;
+import java.awt.BorderLayout;
+import java.net.URL;
+/**
+ * Provides a JFrame with a menu, a tool bar, a mainwindow and a status bar.
+ * The class also provides access to resources.
+ * @author C.Miller
+ * @version 1.0
+ */
+
+
+public class ApplicationFrame extends JFrame {
+ private PackageResourceAdapter ra;
+ private String appName;
+ private JMenuBar mb;
+ private JToolBar tb;
+ private JLabel messages;
+ private HashMap menuMapping;
+ private HashMap menuItemLocation;
+ private HashMap menuItemMapping;
+ private HashMap buttonMapping;
+ private JPanel contentPane;
+ private JComponent contents;
+ public ApplicationFrame() {
+ this(null);
+ }
+
+ /**
+ * Create an Application frame with the resources specified.
+ * <ul>
+ * <li> will try to get a title for the frame from the property message.appName.title
+ * <li> will try to get a URL to show in the initial content pane from helpURL.appName.initialSplash
+ * <li> stops window closing with a dialog box - lables this using message.appName.quit and message.appName.quitTitle
+ * </ul>
+ * @param resourceName looks in the package resources.locale.<resourceName> for a properties file
+ */
+ public ApplicationFrame(String resourceName) {
+ super();
+ appName = resourceName;
+ menuMapping = new HashMap();
+ menuItemMapping = new HashMap();
+ menuItemLocation = new HashMap();
+ buttonMapping = new HashMap();
+ try {
+ ra = new PackageResourceAdapter(resourceName);
+ }
+ catch(IOException e) {
+ throw new RuntimeException("Couldn't find resource file 'resources.locale.' + resourceName + '.properties.");
+ }
+ this.setTitle(ra.getMessageString(appName + ".title"));
+ initGUI();
+ }
+
+ private void initGUI() {
+ final JFrame f = this;
+ // window closing
+ addWindowListener(new WindowAdapter() {
+ public void windowClosing(WindowEvent e) {
+ int n = JOptionPane.showConfirmDialog(f,ra.getMessageString(appName + ".quit"),
+ ra.getMessageString(appName + ".quitTitle"),
+ JOptionPane.YES_NO_OPTION);
+ if(n == JOptionPane.YES_OPTION) {
+ System.err.println("Bye.");
+ System.exit(0);
+ }
+ }
+ });
+
+ setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
+
+
+ // menu bar
+ mb = new JMenuBar();
+ mb.setPreferredSize(new Dimension(200, 20));
+ this.setJMenuBar(mb);
+ // tool bar
+ tb = new JToolBar();
+ tb.setBorder(BorderFactory.createRaisedBevelBorder());
+
+ // main content pane
+ contentPane = new JPanel();
+ contentPane.setLayout(new BorderLayout());
+ contentPane.add(tb, BorderLayout.NORTH);
+
+ // initial splash
+ showInitialSplash();
+ // the messages window at the botton
+
+ messages = new JLabel(ra.getMessageString(appName + ".initMessage"));
+ messages.setBorder(BorderFactory.createLoweredBevelBorder());
+
+ JPanel statusBar = new JPanel();
+ statusBar.setBorder(BorderFactory.createRaisedBevelBorder());
+ statusBar.setLayout(new BorderLayout());
+ statusBar.add(messages, BorderLayout.CENTER);
+ contentPane.add(statusBar, BorderLayout.SOUTH);
+ setContentPane(contentPane);
+ pack();
+ setVisible(true);
+ }
+
+ /**
+ * add a menu with the specified text label.
+ * @param resourceName use the text specified in ApplicationFrame.Menu.<resource name>
+ */
+ public JMenu addMenu(String resourceName) {
+ String text;
+ text=ra.getMessageString(appName + ".Menu." + resourceName);
+ JMenu m = new JMenu(text);
+ menuMapping.put(resourceName,m);
+ mb.add(m);
+ return m;
+ }
+
+
+ /**
+ * remove a menu with the specified text label.
+ * @param resourceName use the text specified in ApplicationFrame.Menu.<resource name>
+ */
+ public JMenu removeMenu(String resourceName) {
+ JMenu m = (JMenu) menuMapping.remove(resourceName);
+ if(m != null) {
+ mb.remove(m);
+ }
+ else throw new IllegalArgumentException("Can't find menu with resourceName " + resourceName);
+ return m;
+ }
+
+ /**
+ * create a menu with the specified text label.
+ * @param menuName add to the specified menu
+ * @param menuItemName use the text specified in ApplicationFrame.MenuItem.<resource name>
+ */
+ public JMenuItem addMenuItem(String menuName, String menuItemName) throws IllegalArgumentException {
+ String text;
+ JMenuItem mi;
+ text=ra.getMessageString(appName + ".MenuItem." + menuItemName);
+ JMenu m = (JMenu) menuMapping.get(menuName);
+ if(m != null) {
+ mi = new JMenuItem(text);
+ menuItemMapping.put(menuItemName,mi);
+ m.add(mi);
+ menuItemLocation.put(menuItemName,menuName);
+ }
+ else throw new IllegalArgumentException("Can't find menu with resourceName " + menuName);
+ return mi;
+ }
+
+ /**
+ * remove a menu item with the specified text label.
+ * @param menuName add to the specified menu
+ * @param menuItemName use the text specified in ApplicationFrame.MenuItem.<resource name>
+ */
+ public JMenuItem removeMenuItem(String menuItemName) throws IllegalArgumentException {
+ String text;
+ JMenuItem mi = (JMenuItem) menuItemMapping.remove(menuItemName);
+ if(mi != null) {
+ String mname = (String) menuItemLocation.remove(menuItemName);
+ JMenu m = (JMenu) menuMapping.get(mname);
+ m.remove(mi);
+ }
+ else throw new IllegalArgumentException("Can't find menu with resourceName " + menuItemName);
+ return mi;
+ }
+
+ /**
+ * create a menu with the specified text label.
+ * @param menuName add to the specified menu
+ * @param menuName use the text specified in ApplicationFrame.Menu.<resource name>
+ */
+ public JMenu addSubMenu(String menuName, String menuItemName) throws IllegalArgumentException {
+ String text;
+ JMenu mi;
+ text=ra.getMessageString(appName + ".Menu." + menuItemName);
+ JMenu m = (JMenu) menuMapping.get(menuName);
+ if(m != null) {
+ mi = new JMenu(text);
+ menuMapping.put(menuItemName,mi);
+ m.add(mi);
+ }
+ else throw new IllegalArgumentException("Can't find menu with resourceName " + menuName);
+ return mi;
+ }
+
+ public void setMenuEnabled(String menuName, boolean enabled) throws IllegalArgumentException {
+ JMenu m = (JMenu) menuMapping.get(menuName);
+ if(m != null) {
+ m.setEnabled(enabled);
+ }
+ else throw new IllegalArgumentException("Can't find menu with resourceName " + menuName);
+ }
+
+
+ public void setMenuItemEnabled(String menuItemName, boolean enabled) throws IllegalArgumentException {
+ JMenuItem m = (JMenu) menuItemMapping.get(menuItemName);
+ if(m != null) {
+ m.setEnabled(enabled);
+ }
+ else throw new IllegalArgumentException("Can't find menuitem with resourceName " + menuItemName);
+ }
+
+
+ /**
+ * add a button with the specified text label.
+ * @param labelName use the text specified in ApplicationFrame.Button.label<resource name>
+ */
+ public JButton addButton(String labelName) throws IllegalArgumentException {
+ String text;
+ text=ra.getMessageString(appName + ".Button." + labelName);
+ JButton b = new JButton(text);
+ buttonMapping.put(labelName,b);
+ tb.add(b);
+ tb.invalidate();
+ return b;
+ }
+
+ /**
+ * add a button with the specified text label. and icon
+ * @param labelName use the text specified in message.<app_name>.Button.label<resource name>
+ * @param iconName use the image specified in image.<app_name>.Button.label<resource name>
+ */
+ public JButton addButton(String labelName, String iconName) throws IllegalArgumentException {
+ String text;
+ ImageIcon ii;
+ text=ra.getMessageString(appName + ".Button." + labelName);
+ ii=new ImageIcon(ra.getImageURL(appName + ".Button." + iconName));
+ JButton b = new JButton(text,ii);
+ buttonMapping.put(labelName,b);
+ tb.add(b);
+ tb.invalidate();
+ return b;
+ }
+
+ /**
+ * add a button with the specified text label, icon and tooltip.
+ * @param labelName use the text specified in message.<app_name>.Button.label<resource name>
+ * @param iconName use the image specified in image.<app_name>.Button.label<resource name>
+ * @param tooltipName use the text specified in tooltip.<app_name>.Button.label<resource name>
+ */
+ public JButton addButton(String labelName, String iconName, String tooltipName) throws IllegalArgumentException {
+ String text;
+ ImageIcon ii;
+ text=ra.getMessageString(appName + ".Button." + labelName);
+ ii=new ImageIcon(ra.getImageURL(appName + ".Button." + iconName));
+ JButton b = new JButton(text,ii);
+ b.setToolTipText(ra.getToolTip(appName + ".Button." + iconName));
+ buttonMapping.put(labelName,b);
+ tb.add(b);
+ tb.invalidate();
+ return b;
+ }
+
+
+ /**
+ * add a button with the specified text label.
+ * @param labelName use the text specified in ApplicationFrame.Button.label<resource name>
+ */
+ public JToggleButton addToggleButton(String labelName) throws IllegalArgumentException {
+ String text;
+ text=ra.getMessageString(appName + ".Button." + labelName);
+ JToggleButton b = new JToggleButton(text);
+ buttonMapping.put(labelName,b);
+ tb.add(b);
+ tb.invalidate();
+ return b;
+ }
+
+ /**
+ * add a button with the specified text label. and icon
+ * @param labelName use the text specified in message.<app_name>.Button.label<resource name>
+ * @param iconName use the image specified in image.<app_name>.Button.label<resource name>
+ */
+ public JToggleButton addToggleButton(String labelName, String iconName) throws IllegalArgumentException {
+ String text;
+ ImageIcon ii;
+ text=ra.getMessageString(appName + ".Button." + labelName);
+ ii=new ImageIcon(ra.getImageURL(appName + ".Button." + iconName));
+ JToggleButton b = new JToggleButton(text,ii);
+ buttonMapping.put(labelName,b);
+ tb.add(b);
+ tb.invalidate();
+ return b;
+ }
+
+ /**
+ * add a button with the specified text label, icon and tooltip.
+ * @param labelName use the text specified in message.<app_name>.Button.label<resource name>
+ * @param iconName use the image specified in image.<app_name>.Button.label<resource name>
+ * @param tooltipName use the text specified in tooltip.<app_name>.Button.label<resource name>
+ */
+ public JToggleButton addToggleButton(String labelName, String iconName, String tooltipName) throws IllegalArgumentException {
+ String text;
+ ImageIcon ii;
+ text=ra.getMessageString(appName + ".Button." + labelName);
+ ii=new ImageIcon(ra.getImageURL(appName + ".Button." + iconName));
+ JToggleButton b = new JToggleButton(text,ii);
+ b.setToolTipText(ra.getToolTip(appName + ".Button." + iconName));
+ buttonMapping.put(labelName,b);
+ tb.add(b);
+ tb.invalidate();
+ return b;
+ }
+
+
+ /**
+ * remove a menu with the specified text label.
+ * @param resourceName use the text specified in ApplicationFrame.Menu.<resource name>
+ */
+ public JButton removeButton(String labelName) throws IllegalArgumentException {
+ JButton b = (JButton) buttonMapping.remove(labelName);
+ if(b != null) {
+ tb.remove(b);
+ }
+ else throw new IllegalArgumentException("Can't find menu with resourceName " + labelName);
+ return b;
+ }
+
+ public void showInitialSplash() {
+
+ // set up the initial splash to show in the main window
+ URL page = ra.getHelpURL(appName + ".initialSplash");
+ JEditorPane initialSplash = new JEditorPane();
+ initialSplash.setEditable(false);
+ try {
+ initialSplash.setPage(page);
+ initialSplash.setPreferredSize(new Dimension(200,100));
+ } catch (IOException e) {
+ System.err.println("Couldn't find initial splash page.\n" + e.getMessage());
+ }
+ setContents(initialSplash);
+ }
+
+ public PackageResourceAdapter getResourceAdapter() {
+ return ra;
+ }
+
+ public void setContents(JComponent c) {
+ if(contents != null) {
+ contentPane.remove(contents);
+ }
+ contentPane.add(c, BorderLayout.CENTER);
+ contents = c;
+ contentPane.revalidate();
+ contentPane.repaint();
+ }
+
+ public JComponent getContents() {
+ return contents;
+ }
+
+ public void showMessage(String message) {
+ messages.setText(message);
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.java b/src/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.java
new file mode 100644
index 0000000..6808d74
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/PopUpHtmlDisplay.java
@@ -0,0 +1,61 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util;
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import java.net.URL;
+import java.io.IOException;
+
+
+/**
+ * Displays an URL with a single 'OK' button at the bottom
+ */
+public class PopUpHtmlDisplay {
+
+ private PopUpHtmlDisplay() {
+ }
+
+ public static void show(Component frame, URL page){
+ final JComponent pageC = getPage(page);
+ JOptionPane.showMessageDialog(frame,pageC);
+ }
+
+
+ /**
+ * try to open the URL and get the page
+ */
+ public static final JComponent getPage(URL page) {
+ JPanel contentPane = new JPanel();
+ contentPane.setLayout(new BorderLayout());
+
+ JEditorPane editorPane = new JEditorPane();
+ editorPane.setEditable(false);
+ editorPane.setPreferredSize(new Dimension(400, 400));
+ editorPane.setMinimumSize(new Dimension(400, 400));
+
+ JScrollPane editorScrollPane = new JScrollPane(editorPane);
+ try {
+ editorPane.setPage(page);
+ } catch (IOException e) {
+ System.err.println("Attempted to read a bad URL: " + page);
+ }
+
+ contentPane.add(editorPane, BorderLayout.CENTER);
+ return contentPane;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/SwingWorker.java b/src/uk/ac/man/bioinf/gui/util/SwingWorker.java
new file mode 100644
index 0000000..1ff2da7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/SwingWorker.java
@@ -0,0 +1,147 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.util;
+import javax.swing.SwingUtilities;
+
+/**
+ * This is the 3rd version of SwingWorker (also known as
+ * SwingWorker 3), an abstract class that you subclass to
+ * perform GUI-related work in a dedicated thread. For
+ * instructions on using this class, see:
+ *
+ * http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html
+ *
+ * Note that the API changed slightly in the 3rd version:
+ * You must now invoke start() on the SwingWorker after
+ * creating it.
+ */
+public abstract class SwingWorker {
+ private Object value; // see getValue(), setValue()
+ private Thread thread;
+
+ /**
+ * Class to maintain reference to current worker thread
+ * under separate synchronization control.
+ */
+ private static class ThreadVar {
+ private Thread thread;
+ ThreadVar(Thread t) { thread = t; }
+ synchronized Thread get() { return thread; }
+ synchronized void clear() { thread = null; }
+ }
+
+ private ThreadVar threadVar;
+
+ /**
+ * Get the value produced by the worker thread, or null if it
+ * hasn't been constructed yet.
+ */
+ protected synchronized Object getValue() {
+ return value;
+ }
+
+ /**
+ * Set the value produced by worker thread
+ */
+ private synchronized void setValue(Object x) {
+ value = x;
+ }
+
+ /**
+ * Compute the value to be returned by the <code>get</code> method.
+ */
+ public abstract Object construct();
+
+ /**
+ * Called on the event dispatching thread (not on the worker thread)
+ * after the <code>construct</code> method has returned.
+ */
+ public void finished() {
+ }
+
+ /**
+ * A new method that interrupts the worker thread. Call this method
+ * to force the worker to stop what it's doing.
+ */
+ public void interrupt() {
+ Thread t = threadVar.get();
+ if (t != null) {
+ t.interrupt();
+ }
+ threadVar.clear();
+ }
+
+ /**
+ * Return the value created by the <code>construct</code> method.
+ * Returns null if either the constructing thread or the current
+ * thread was interrupted before a value was produced.
+ *
+ * @return the value created by the <code>construct</code> method
+ */
+ public Object get() {
+ while (true) {
+ Thread t = threadVar.get();
+ if (t == null) {
+ return getValue();
+ }
+ try {
+ t.join();
+ }
+ catch (InterruptedException e) {
+ Thread.currentThread().interrupt(); // propagate
+ return null;
+ }
+ }
+ }
+
+
+ /**
+ * Start a thread that will call the <code>construct</code> method
+ * and then exit.
+ */
+ public SwingWorker() {
+ final Runnable doFinished = new Runnable() {
+ public void run() { finished(); }
+ };
+
+ Runnable doConstruct = new Runnable() {
+ public void run() {
+ try {
+ setValue(construct());
+ }
+ finally {
+ threadVar.clear();
+ }
+
+ SwingUtilities.invokeLater(doFinished);
+ }
+ };
+
+ Thread t = new Thread(doConstruct);
+ threadVar = new ThreadVar(t);
+ }
+
+ /**
+ * Start the worker thread.
+ */
+ public void start() {
+ Thread t = threadVar.get();
+ if (t != null) {
+ t.start();
+ }
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/TripletPanel.java b/src/uk/ac/man/bioinf/gui/util/TripletPanel.java
new file mode 100644
index 0000000..57a3d4b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/TripletPanel.java
@@ -0,0 +1,121 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util;
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.JScrollPane;
+import javax.swing.JComponent;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+
+/**
+ * Triplet panel provides a GUI Component with three sub components.
+ * There is a main window on the right handsied and two sub windows on the left.
+ * The relative sacing of these windows is controlled by split panes.
+ * Methods exist to add and remove Components from these windows.
+ * @author C. Miller
+ * @version $Id :
+ */
+
+public class TripletPanel extends JPanel {
+ private JSplitPane leftRightSplit;
+ private JSplitPane upDownSplit;
+ private JPanel mainWindow;
+ private JPanel topLeft;
+ private JPanel bottomLeft;
+ private JComponent tlt;
+ private JComponent blt;
+ private JComponent rht;
+ private JScrollPane tlp;
+ private JScrollPane blp;
+ private JScrollPane rhp;
+
+
+
+ public TripletPanel() {
+ this(new JPanel(), new JPanel(), new JPanel());
+ }
+
+ public TripletPanel(JComponent topLeft, JComponent bottomLeft, JComponent mainWindow) {
+ super();
+ init();
+ setMainWindow(mainWindow);
+ setTopLeft(topLeft);
+ setBottomLeft(bottomLeft);
+ }
+
+ private void init() {
+ this.setLayout(new BorderLayout());
+ topLeft = new JPanel();
+ bottomLeft = new JPanel();
+ mainWindow = new JPanel();
+ topLeft.setLayout(new BorderLayout());
+ bottomLeft.setLayout(new BorderLayout());
+ mainWindow.setLayout(new BorderLayout());
+
+ Dimension minimumSize = new Dimension(100, 50);
+ topLeft.setMinimumSize(minimumSize);
+ bottomLeft.setMinimumSize(minimumSize);
+ mainWindow.setMinimumSize(minimumSize);
+
+ Dimension preferredSize = new Dimension(100, 50);
+ topLeft.setPreferredSize(preferredSize);
+ bottomLeft.setPreferredSize(preferredSize);
+ preferredSize = new Dimension(400, 400);
+ mainWindow.setPreferredSize(preferredSize);
+
+ tlp = new JScrollPane(topLeft);
+ blp = new JScrollPane(bottomLeft);
+ rhp = new JScrollPane(mainWindow);
+
+ upDownSplit = new JSplitPane(JSplitPane.VERTICAL_SPLIT,tlp,blp);
+ leftRightSplit = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,upDownSplit,rhp);
+ upDownSplit.setOneTouchExpandable(true);
+ leftRightSplit.setOneTouchExpandable(true);
+ leftRightSplit.setDividerLocation(150);
+ //Provide minimum sizes for the two components in the split pane
+ this.add(leftRightSplit,BorderLayout.CENTER);
+ }
+
+ public void setMainWindow(JComponent c) {
+ if(rht != null) mainWindow.remove(rht);
+ mainWindow.add(c,BorderLayout.CENTER);
+ rht = c;
+ mainWindow.revalidate();
+ System.err.println("Set main window");
+ }
+
+ public JComponent getMainWindow() { return mainWindow; }
+
+ public void setTopLeft(JComponent c) {
+ if(tlt != null) topLeft.remove(tlt);
+ topLeft.add(c,BorderLayout.CENTER);
+ tlt = c;
+ topLeft.revalidate();
+ }
+
+ public JComponent getTopLeft() { return topLeft; }
+
+ public void setBottomLeft(JComponent c) {
+ if(blt != null) bottomLeft.remove(blt);
+ bottomLeft.add(c,BorderLayout.CENTER);
+ blt = c;
+ bottomLeft.revalidate();
+ }
+
+ public JComponent getBottomLeft() { return bottomLeft; }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/forms/DecimalField.java b/src/uk/ac/man/bioinf/gui/util/forms/DecimalField.java
new file mode 100644
index 0000000..449b2c1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/forms/DecimalField.java
@@ -0,0 +1,73 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util.forms;
+import javax.swing.*;
+import javax.swing.text.*;
+
+import java.awt.Toolkit;
+import java.text.*;
+
+/**
+ * Provides a validated field that only accepts decimal numbers.
+ * @author C.Miller
+ * @version 1.0
+ */
+public class DecimalField extends JTextField {
+ private NumberFormat format;
+
+ public DecimalField(int columns, NumberFormat f) {
+ super(columns);
+ setDocument(new FormattedDocument(f));
+ format = f;
+ }
+
+ public DecimalField(double value, int columns, NumberFormat f) {
+ super(columns);
+ setDocument(new FormattedDocument(f));
+ format = f;
+ setValue(value);
+ }
+
+ public boolean isValid() {
+ try {
+ format.parse(getText()).intValue();
+ } catch (ParseException e) {
+ // This should never happen because insertString allows
+ // only properly formatted data to get in the field.
+ return false;
+ }
+ return true;
+ }
+
+ public double getValue() {
+ double retVal = 0.0;
+
+ try {
+ retVal = format.parse(getText()).doubleValue();
+ } catch (ParseException e) {
+ // This should never happen because insertString allows
+ // only properly formatted data to get in the field.
+ Toolkit.getDefaultToolkit().beep();
+ System.err.println("getValue: could not parse: " + getText());
+ }
+ return retVal;
+ }
+
+ public void setValue(double value) {
+ setText(format.format(value));
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.java b/src/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.java
new file mode 100644
index 0000000..93c3231
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/forms/FormattedDocument.java
@@ -0,0 +1,70 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util.forms;
+import javax.swing.*;
+import javax.swing.text.*;
+
+import java.awt.Toolkit;
+import java.text.*;
+import java.util.Locale;
+
+public class FormattedDocument extends PlainDocument {
+ private Format format;
+
+ public FormattedDocument(Format f) {
+ format = f;
+ }
+
+ public Format getFormat() {
+ return format;
+ }
+
+ public void insertString(int offs, String str, AttributeSet a)
+ throws BadLocationException {
+
+ String currentText = getText(0, getLength());
+ String beforeOffset = currentText.substring(0, offs);
+ String afterOffset = currentText.substring(offs, currentText.length());
+ String proposedResult = beforeOffset + str + afterOffset;
+
+ try {
+ format.parseObject(proposedResult);
+ super.insertString(offs, str, a);
+ } catch (ParseException e) {
+ Toolkit.getDefaultToolkit().beep();
+ System.err.println("insertString: could not parse: "
+ + proposedResult);
+ }
+ }
+
+ public void remove(int offs, int len) throws BadLocationException {
+ String currentText = getText(0, getLength());
+ String beforeOffset = currentText.substring(0, offs);
+ String afterOffset = currentText.substring(len + offs,
+ currentText.length());
+ String proposedResult = beforeOffset + afterOffset;
+
+ try {
+ if (proposedResult.length() != 0)
+ format.parseObject(proposedResult);
+ super.remove(offs, len);
+ } catch (ParseException e) {
+ Toolkit.getDefaultToolkit().beep();
+ System.err.println("remove: could not parse: " + proposedResult);
+ }
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/forms/IntegerField.java b/src/uk/ac/man/bioinf/gui/util/forms/IntegerField.java
new file mode 100644
index 0000000..ab8520a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/forms/IntegerField.java
@@ -0,0 +1,97 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util.forms;
+import javax.swing.*;
+import javax.swing.text.*;
+
+import java.awt.Toolkit;
+import java.text.NumberFormat;
+import java.text.ParseException;
+import java.util.Locale;
+
+public class IntegerField extends JTextField {
+ private Toolkit toolkit;
+ private NumberFormat integerFormatter;
+
+ public IntegerField(int columns) {
+ super(columns);
+ toolkit = Toolkit.getDefaultToolkit();
+ integerFormatter = NumberFormat.getNumberInstance(Locale.US);
+ integerFormatter.setParseIntegerOnly(true);
+ }
+
+
+ public IntegerField(int value, int columns) {
+ super(columns);
+ toolkit = Toolkit.getDefaultToolkit();
+ integerFormatter = NumberFormat.getNumberInstance(Locale.US);
+ integerFormatter.setParseIntegerOnly(true);
+ setValue(value);
+ }
+
+ public boolean isValid() {
+ try {
+ integerFormatter.parse(getText()).intValue();
+ } catch (ParseException e) {
+ // This should never happen because insertString allows
+ // only properly formatted data to get in the field.
+ return false;
+ }
+ return true;
+ }
+
+ public int getValue() {
+ int retVal = 0;
+ try {
+ retVal = integerFormatter.parse(getText()).intValue();
+ } catch (ParseException e) {
+ // This should never happen because insertString allows
+ // only properly formatted data to get in the field.
+ toolkit.beep();
+ }
+ return retVal;
+ }
+
+ public void setValue(int value) {
+ setText(integerFormatter.format(value));
+ }
+
+ protected Document createDefaultModel() {
+ return new IntegerDocument();
+ }
+
+ protected class IntegerDocument extends PlainDocument {
+ public void insertString(int offs,
+ String str,
+ AttributeSet a)
+ throws BadLocationException {
+ char[] source = str.toCharArray();
+ char[] result = new char[source.length];
+ int j = 0;
+
+ for (int i = 0; i < result.length; i++) {
+ if (Character.isDigit(source[i]) || source[i]=='-' || source[i]=='+')
+ result[j++] = source[i];
+ else {
+ toolkit.beep();
+ System.err.println("insertString: " + source[i]);
+ }
+ }
+ super.insertString(offs, new String(result, 0, j), a);
+ }
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.java b/src/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.java
new file mode 100644
index 0000000..2d9bb02
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/forms/PasswordDialog.java
@@ -0,0 +1,139 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util.forms;
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import java.net.URL;
+import java.io.IOException;
+
+
+/**
+ * Pop up Dialog box to get a password off a user.
+ * @author C.Miller
+ * @version 1.0
+ */
+public class PasswordDialog {
+ protected JFrame parent;
+ protected JTextField userName;
+ protected JPasswordField password;
+ protected JCheckBox remember;
+ JLabel un;
+ JLabel pw;
+
+ public PasswordDialog(JFrame parent) {
+ userName = new JTextField();
+ password = new JPasswordField();
+ }
+
+ public PasswordDialog(JFrame parent, String userNameLabel, String passwordLabel) {
+ this.parent = parent;
+ userName = new JTextField();
+ password = new JPasswordField();
+ remember = new JCheckBox("Remember password?");
+ un = new JLabel("Username");
+ pw = new JLabel("Password");
+ }
+
+ public PasswordDialog(JFrame parent, String userNameLabel, String passwordLabel, String initialUserName, String initialPassword) {
+ this.parent = parent;
+ userName = new JTextField();
+ password = new JPasswordField();
+ remember = new JCheckBox("Remember password?");
+ un = new JLabel(userNameLabel);
+ pw = new JLabel(passwordLabel);
+ }
+
+ public PasswordDialog(JFrame parent, String userNameLabel, String passwordLabel, String rememberLabel,
+ String initialUserName, String initialPassword, boolean initialRemember) {
+ this.parent = parent;
+ userName = new JTextField(initialUserName);
+ password = new JPasswordField(initialPassword);
+ remember = new JCheckBox(rememberLabel);
+ remember.setSelected(initialRemember);
+ un = new JLabel(userNameLabel);
+ pw = new JLabel(passwordLabel);
+ }
+
+ public void show() {
+ JOptionPane.showMessageDialog(parent, getPasswordPane());
+ }
+
+ private void addRows(JComponent[] col1,
+ JComponent[] col2,
+ GridBagLayout gridbag,
+ Container container) {
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.EAST;
+ int numCols = col1.length;
+
+ for (int i = 0; i < numCols; i++) {
+ c.gridwidth = GridBagConstraints.RELATIVE; //next-to-last
+ c.fill = GridBagConstraints.NONE; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(col1[i], c);
+ container.add(col1[i]);
+
+ c.gridwidth = GridBagConstraints.REMAINDER; //end row
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ gridbag.setConstraints(col2[i], c);
+ container.add(col2[i]);
+ }
+ }
+
+ public char[] getPassword() {
+ return password.getPassword();
+ }
+
+ public String getUserName() {
+ return userName.getText();
+ }
+
+ public void setPassword(String pw) {
+ password.setText(pw);
+ }
+
+ public void setUserName(String un) {
+ userName.setText(un);
+ }
+
+ public boolean isPasswordToBeRemembered() {
+ return remember.isSelected();
+ }
+
+ public void setRememberPassword(boolean r) {
+ remember.setSelected(r);
+ }
+
+ public JComponent getPasswordPane() {
+ JPanel contentPane = new JPanel();
+ GridBagLayout layout = new GridBagLayout();
+ contentPane.setLayout(layout);
+ JComponent[] col1 = {un,pw};
+ JComponent[] col2 = {userName,password};
+ addRows(col1,col2,layout,contentPane);
+ GridBagConstraints c = new GridBagConstraints();
+ c.anchor = GridBagConstraints.EAST;
+ c.gridwidth = GridBagConstraints.REMAINDER; //end row
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ layout.setConstraints(remember, c);
+ contentPane.add(remember);
+ return contentPane;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.java b/src/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.java
new file mode 100644
index 0000000..dd9bb3d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/forms/ValidatedForm.java
@@ -0,0 +1,414 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util.forms;
+import javax.swing.*;
+import javax.swing.text.*;
+import javax.swing.event.*;
+import java.awt.Toolkit;
+import java.text.NumberFormat;
+import java.text.DecimalFormat;
+import java.text.ParseException;
+import java.util.*;
+import java.awt.event.*;
+import java.awt.*;
+import javax.swing.*;
+
+
+public class ValidatedForm extends JPanel {
+ private HashMap labels;
+ private HashMap fields;
+ private HashMap modifiers;
+ private HashMap changes;
+ private GridBagConstraints c;
+ private GridBagLayout gridbag;
+ private int currentRow;
+ private MyDocumentListener myDocumentListener;
+
+ public static final int LESS_THAN = 0;
+ public static final int GREATER_THAN = 1;
+ public static final int EQUALS = 2;
+ public static final int LIKE = 3;
+
+ public ValidatedForm() {
+ super();
+ labels = new HashMap();
+ fields = new HashMap();
+ modifiers = new HashMap();
+ changes = new HashMap();
+ //text fields on right
+ myDocumentListener = new MyDocumentListener();
+
+ this.setBorder(BorderFactory.createEmptyBorder(20, 20, 20, 20));
+
+
+ c = new GridBagConstraints();
+ gridbag = new GridBagLayout();
+ this.setLayout(gridbag);
+
+ currentRow = 0;
+ c.anchor = GridBagConstraints.EAST;
+ }
+
+ public void addIntegerField(String key, String label, int init, boolean modifier, int columns) {
+ JLabel l = new JLabel(label);
+ labels.put(key,l);
+ IntegerField i = new IntegerField(init,columns);
+ fields.put(key,i);
+ i.getDocument().addDocumentListener(myDocumentListener);
+ i.getDocument().putProperty("name", key);
+ ModifierCombo m = new ModifierCombo(false);
+ if(modifier) modifiers.put(key,m);
+
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.NONE; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(l, c);
+ this.add(l);
+
+ c.gridwidth = 1;
+ c.gridx = 1;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(m, c);
+ this.add(m);
+
+ c.gridwidth = 1;
+ c.gridx = 2;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ gridbag.setConstraints(i, c);
+ this.add(i);
+
+ currentRow++;
+
+ this.revalidate();
+ }
+
+ public void addIntegerField(String key, String label, boolean modifier, int columns) {
+ JLabel l = new JLabel(label);
+ labels.put(key,l);
+ IntegerField i = new IntegerField(columns);
+ fields.put(key,i);
+ i.getDocument().addDocumentListener(myDocumentListener);
+ i.getDocument().putProperty("name", key);
+
+ ModifierCombo m = new ModifierCombo(false);
+ if(modifier) modifiers.put(key,m);
+
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.NONE; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(l, c);
+ this.add(l);
+
+ c.gridwidth = 1;
+ c.gridx = 1;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(m, c);
+ this.add(m);
+
+ c.gridwidth = 1;
+ c.gridx = 2;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ gridbag.setConstraints(i, c);
+ this.add(i);
+
+ currentRow++;
+
+ this.revalidate();
+ }
+
+ public void addDecimalField(String key, String label, double init, boolean modifier, int columns, boolean isPercent) {
+ JLabel l = new JLabel(label);
+ labels.put(key,l);
+ DecimalField i;
+ if(isPercent) {
+ NumberFormat percentFormat = NumberFormat.getNumberInstance();
+ percentFormat.setMinimumFractionDigits(3);
+ //XXXX: Workaround. With an empty positive suffix
+ //the format allows letters in the number.
+ ((DecimalFormat)percentFormat).setPositiveSuffix(" ");
+ i = new DecimalField(init,columns,percentFormat);
+ }
+ else {
+ NumberFormat format = NumberFormat.getNumberInstance();
+
+ i = new DecimalField(init,columns,format);
+ }
+ fields.put(key,i);
+ i.getDocument().addDocumentListener(myDocumentListener);
+ i.getDocument().putProperty("name", key);
+
+ ModifierCombo m = new ModifierCombo(false);
+ if(modifier) modifiers.put(key,m);
+
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.NONE; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(l, c);
+ this.add(l);
+
+ c.gridwidth = 1;
+ c.gridx = 1;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(m, c);
+ this.add(m);
+
+ c.gridwidth = 1;
+ c.gridx = 2;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ gridbag.setConstraints(i, c);
+ this.add(i);
+
+ currentRow++;
+
+ this.revalidate();
+ }
+
+ public void addDecimalField(String key, String label, boolean modifier, int columns, boolean isPercent) {
+ JLabel l = new JLabel(label);
+ labels.put(key,l);
+ DecimalField i;
+ if(isPercent) {
+ NumberFormat percentFormat = NumberFormat.getNumberInstance();
+ percentFormat.setMinimumFractionDigits(3);
+ //XXXX: Workaround. With an empty positive suffix
+ //the format allows letters in the number.
+ ((DecimalFormat)percentFormat).setPositiveSuffix(" ");
+ i = new DecimalField(columns,percentFormat);
+ }
+ else {
+ NumberFormat format = NumberFormat.getNumberInstance();
+
+ i = new DecimalField(columns,format);
+ }
+ fields.put(key,i);
+ i.getDocument().addDocumentListener(myDocumentListener);
+ i.getDocument().putProperty("name", key);
+
+ ModifierCombo m = new ModifierCombo(false);
+ if(modifier) modifiers.put(key,m);
+
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.NONE; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(l, c);
+ this.add(l);
+
+ c.gridwidth = 1;
+ c.gridx = 1;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(m, c);
+ this.add(m);
+
+ c.gridwidth = 1;
+ c.gridx = 2;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ gridbag.setConstraints(i, c);
+ this.add(i);
+
+ currentRow++;
+
+ this.revalidate();
+ }
+
+ public void addTextField(String key, String label, String init, boolean modifier, int columns) {
+ JLabel l = new JLabel(label);
+ labels.put(key,l);
+ JTextField i = new JTextField(init,columns);
+ fields.put(key,i);
+ i.getDocument().addDocumentListener(myDocumentListener);
+ i.getDocument().putProperty("name", key);
+
+ ModifierCombo m = new ModifierCombo(true);
+ if(modifier) modifiers.put(key,m);
+
+ c.gridwidth = 1;
+ c.gridx = 0;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.NONE; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(l, c);
+ this.add(l);
+
+ c.gridwidth = 1;
+ c.gridx = 1;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL; //reset to default
+ c.weightx = 0.0; //reset to default
+ gridbag.setConstraints(m, c);
+ this.add(m);
+
+ c.gridwidth = 1;
+ c.gridx = 2;
+ c.gridy = currentRow;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ c.weightx = 1.0;
+ gridbag.setConstraints(i, c);
+ this.add(i);
+
+ currentRow++;
+
+ this.revalidate();
+ }
+
+ class MyDocumentListener implements DocumentListener {
+ public void insertUpdate(DocumentEvent e) {
+ recordChange(e);
+ }
+ public void removeUpdate(DocumentEvent e) {
+ recordChange(e);
+ }
+ public void changedUpdate(DocumentEvent e) {
+ // we won't ever get this with a PlainDocument
+ }
+ private void recordChange(DocumentEvent e) {
+ }
+ }
+
+
+ public int getIntegerFieldValue(String key) {
+ IntegerField i = (IntegerField) fields.get(key);
+ return i.getValue();
+ }
+
+ public double getDecimalFieldValue(String key) {
+ DecimalField d = (DecimalField) fields.get(key);
+ return d.getValue();
+ }
+
+ public String getTextFieldValue(String key) {
+ JTextField t = (JTextField) fields.get(key);
+ return t.getText();
+ }
+
+ public boolean isIntegerFieldValid(String key) {
+ IntegerField i = (IntegerField) fields.get(key);
+ return i.isValid();
+ }
+
+ public boolean isDecimalFieldValid(String key) {
+ DecimalField d = (DecimalField) fields.get(key);
+ return d.isValid();
+ }
+
+ public boolean isTextFieldValid(String key) {
+ JTextField t = (JTextField) fields.get(key);
+ return (!t.getText().equals(""));
+ }
+
+ public void setIntegerFieldValue(String key, int v) {
+ IntegerField i = (IntegerField) fields.get(key);
+ i.setValue(v);
+ }
+
+ public void setDecimalFieldValue(String key, double v) {
+ DecimalField d = (DecimalField) fields.get(key);
+ d.setValue(v);
+ }
+
+ public void setTextFieldValue(String key, String v) {
+ JTextField t = (JTextField) fields.get(key);
+ t.setText(v);
+ }
+
+ public int getModifierType(String key) {
+ ModifierCombo mc = (ModifierCombo) modifiers.get(key);
+ String text = (String)mc.getSelectedItem();
+ if(text.equals("<")) {
+ return ValidatedForm.LESS_THAN;
+ }
+ else if(text.equals(">")) {
+ return ValidatedForm.GREATER_THAN;
+ }
+ else if(text.equals("=")) {
+ return ValidatedForm. EQUALS;
+ }
+ else if(text.equals("equals")) {
+ return ValidatedForm.EQUALS;
+ }
+ else {
+ return ValidatedForm.LIKE;
+ }
+ }
+
+ public void setModifierType(String key, int t) {
+ ModifierCombo mc = (ModifierCombo) modifiers.get(key);
+ switch(t) {
+ case ValidatedForm.LESS_THAN:
+ mc.setSelectedIndex(0);
+ break;
+ case ValidatedForm.GREATER_THAN:
+ mc.setSelectedIndex(1);
+ break;
+ case ValidatedForm.EQUALS:
+ mc.setSelectedIndex(2);
+ break;
+ case ValidatedForm.LIKE:
+ mc.setSelectedIndex(3);
+ break;
+ default:
+ throw new IllegalArgumentException("Modifier type out of range!");
+ }
+
+ }
+
+ private class ModifierCombo extends JComboBox {
+
+ public ModifierCombo(boolean text) {
+ super();
+ if(text) initText();
+ else initNumber();
+ }
+
+ private void initText() {
+ this.addItem("equals");
+ this.addItem("like");
+ }
+
+
+ private void initNumber() {
+ this.addItem("=");
+ this.addItem("<");
+ this.addItem(">");
+ }
+
+ }
+
+}
diff --git a/src/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.java b/src/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.java
new file mode 100644
index 0000000..a632571
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/util/forms/WholeNumberField.java
@@ -0,0 +1,82 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.util.forms;
+import javax.swing.*;
+import javax.swing.text.*;
+
+import java.awt.Toolkit;
+import java.text.NumberFormat;
+import java.text.ParseException;
+import java.util.Locale;
+
+/**
+ * @author C.Miller
+ * @version $Id: WholeNumberField.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+public class WholeNumberField extends JTextField {
+ private Toolkit toolkit;
+ private NumberFormat integerFormatter;
+
+ public WholeNumberField(int value, int columns) {
+ super(columns);
+ toolkit = Toolkit.getDefaultToolkit();
+ integerFormatter = NumberFormat.getNumberInstance(Locale.US);
+ integerFormatter.setParseIntegerOnly(true);
+ setValue(value);
+ }
+
+ public int getValue() {
+ int retVal = 0;
+ try {
+ retVal = integerFormatter.parse(getText()).intValue();
+ } catch (ParseException e) {
+ // This should never happen because insertString allows
+ // only properly formatted data to get in the field.
+ toolkit.beep();
+ }
+ return retVal;
+ }
+
+ public void setValue(int value) {
+ setText(integerFormatter.format(value));
+ }
+
+ protected Document createDefaultModel() {
+ return new WholeNumberDocument();
+ }
+
+ protected class WholeNumberDocument extends PlainDocument {
+ public void insertString(int offs,
+ String str,
+ AttributeSet a)
+ throws BadLocationException {
+ char[] source = str.toCharArray();
+ char[] result = new char[source.length];
+ int j = 0;
+
+ for (int i = 0; i < result.length; i++) {
+ if (Character.isDigit(source[i]))
+ result[j++] = source[i];
+ else {
+ toolkit.beep();
+ System.err.println("insertString: " + source[i]);
+ }
+ }
+ super.insertString(offs, new String(result, 0, j), a);
+ }
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.java b/src/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.java
new file mode 100644
index 0000000..c9399ca
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionModel.java
@@ -0,0 +1,151 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+
+
+/**
+ * AlignmentSelectionModel.java
+ *
+ * This defines the selection model for the JAlignmentViewer. The main
+ * three methods of this class, namely stopSelection(),
+ * extendSelection() and clearSelection() are called by the
+ * JAlignmentViewer, or one of its helper classes and usually
+ * considered to be advisory. The model is free to ignore these method
+ * calls if it is appropriate behaviour.
+ *
+ * Created: Mon Apr 10 11:32:26 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentSelectionModel.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface AlignmentSelectionModel
+{
+ /**
+ * is the current selection in the process of being selected.
+ * @return true is selection is changing
+ */
+ public boolean isSelecting();
+
+ /**
+ * Returns the current selection or null if there is no
+ * selection. If there is more than one selection this should return
+ * the most recently made selection
+ * @return the selection
+ */
+ public SequenceAlignmentRectangle getCurrentSelection();
+
+ /**
+ * Get the number of selections.
+ * @return the number of selections
+ */
+ public int getNumberSelections();
+
+ /**
+ * Gets the given selection. The index should reflect the
+ * chronological order in which the selections were made, with the
+ * smallest index first
+ * @param index the index
+ * @return the selection array index at the given index
+ * @exception ArrayIndexOutOfBoundsException if the index is out of bounds
+ */
+ public SequenceAlignmentRectangle getSelectionAt( int index )
+ throws IndexOutOfBoundsException;
+
+ /**
+ * Is the point within one of the selection rectangles
+ * @param point the point
+ * @return true if point is within a rectangle
+ */
+ public boolean isPointSelected( SequenceAlignmentPoint point );
+
+ /**
+ * Clear all the selections in this model
+ */
+ public void clearSelection();
+
+ /**
+ * Get the first selection rectangle which surrounds the point, or
+ * null if there is not one.
+ * @param point the point in question
+ * @return the rectangle surrounding point
+ */
+ public SequenceAlignmentRectangle getRectangleAtPoint( SequenceAlignmentPoint point );
+
+ /**
+ * Get all selection rectangles which surround this point, or null
+ * if there is not one
+ * @param point the point in question
+ * @return the rectangles surrounding point
+ */
+ public SequenceAlignmentRectangle[] getRectanglesAtPoint( SequenceAlignmentPoint point );
+
+ /**
+ * Start a selection at the given point
+ * @param point the start of the selection
+ */
+ public void extendSelection( SequenceAlignmentPoint point );
+
+ /**
+ * Complete the selection at the given point
+ * @param point the point to complete the selection
+ */
+ public void stopSelection( SequenceAlignmentPoint point );
+
+ public void addAlignmentSelectionListener( AlignmentSelectionListener listener );
+
+ public void removeAlignmentSelectionListener( AlignmentSelectionListener listener );
+
+} // AlignmentSelectionModel
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentSelectionModel.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/01/15 18:54:21 lord
+ * Changed exception type to less specific one.
+ * Removed one method which seems extraneous.
+ *
+ * Revision 1.2 2001/01/04 14:55:56 lord
+ * Extended documentation
+ *
+ * Revision 1.1 2000/04/18 17:43:55 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/11 16:56:23 lord
+ * Initial version. It compiles, but that does not mean it works
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.java
new file mode 100644
index 0000000..3f3b862
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/AlignmentSelectionRenderer.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import java.awt.Graphics;
+
+
+/**
+ * SelectionRenderer.java
+ *
+ *
+ * Created: Wed Mar 7 18:45:50 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentSelectionRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface AlignmentSelectionRenderer
+{
+ public void renderAlignmentSelection
+ ( Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, SequenceAlignmentRectangle rect );
+
+} // SelectionRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentSelectionRenderer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/03/12 16:34:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..6ee30ed
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/AlignmentViewerCellRenderer.java
@@ -0,0 +1,97 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.Component;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import java.awt.Color;
+
+/**
+ * AlignmentViewerCellRenderer.java
+ *
+ * Initial interface for the AlignmentViewerCellRender. This defines a
+ * component which is used to render an individual cell for a
+ * JAlignmentViewer. Its not complete yet. Its needs information about
+ * the colour model to be used for this cell. And possible info about
+ * the difference between the alignment position, and the viewer
+ * position, Im not sure.
+ *
+ * Created: Mon Mar 20 15:50:14 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentViewerCellRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface AlignmentViewerCellRenderer
+{
+ /**
+ * This method should be able to cope with null values for element
+ * which will be passed if we are off the front or the end of the sequence
+ * @param viewer
+ * @param element
+ * @param sequenceIndex
+ * @param bgColor the background color of the cell (can be null)
+ * @param isSelected
+ * @param cellHasFocus
+ * @return
+ */
+ public Component getAlignmentViewerCellRendererComponent
+ ( JAlignmentViewer viewer,
+ Element element,
+ SequenceAlignmentPoint location,
+ Color bgColor,
+ boolean isSelected,
+ boolean hasFocus,
+ boolean isAtPoints );
+}// AlignmentViewerCellRenderer
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentViewerCellRenderer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:43:55 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.4 2000/04/12 13:41:13 jns
+ * o added in color mapping code
+ *
+ * Revision 1.3 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.2 2000/03/29 15:50:47 lord
+ * Updated to use new sequence.geom package
+ *
+ * Revision 1.1 2000/03/21 14:41:39 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..b9476ec
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/BorderFastAlignmentViewerCellRenderer.java
@@ -0,0 +1,103 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.awt.Graphics;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * BorderFastAlignmentViewerCellRenderer.java
+ *
+ * One of three classes designed to render cells in the
+ * JAlignmentViewer. This one deals specifically with the border to
+ * the cell.
+ * <p>
+ * By default, it will probably be drawn second (after the color), but
+ * all of this is determined by the RendererManager.
+ *
+ * Created: Fri Aug 25 14:06:17 2000
+ *
+ * @author Julian Selley
+ * @version $Id: BorderFastAlignmentViewerCellRenderer.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class BorderFastAlignmentViewerCellRenderer
+ implements FastAlignmentViewerCellRenderer
+{
+ public BorderFastAlignmentViewerCellRenderer() {}
+
+ public void renderAlignmentViewerCell
+ (Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color color,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint)
+ {
+ /* decide on the color of the border based on the supplied
+ * booleans
+ */
+ if ( element == null || element == Gap.GAP )
+ g.setColor(viewer.getBackground());
+ else
+ g.setColor(Color.black);
+ if (isSelected)
+ g.setColor(Color.red);
+ if (isAtPoint)
+ g.setColor(Color.green);
+
+ /* (PENDING: JNS 25.8.00) currently this only draws a border of
+ * width 1 (or whatever the graphics drawRect is set to do). It
+ * would be nice to later on specify the width of the border.
+ */
+ // draw the border
+ g.drawRect(x, y, width - 1, height - 1);
+ }
+} // BorderFastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: BorderFastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/10/03 17:13:20 lord
+ * Now cope with Gap elements correctly
+ *
+ * Revision 1.2 2000/09/19 14:57:33 jns
+ * o making the borders draw properly
+ *
+ * Revision 1.1 2000/09/18 17:54:54 jns
+ * o created a new multiplexer cell renderer to take account of cell size
+ * o initial code
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.java b/src/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.java
new file mode 100644
index 0000000..a148759
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/ButtonViewerPopupMenu.java
@@ -0,0 +1,99 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.Point;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import javax.swing.JLabel;
+import javax.swing.JPopupMenu;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+
+/**
+ * ButtonViewerPopupMenu.java
+ *
+ * This class implements a pop up menu for the
+ * JAlignmentButtonPanel. The top menu item gives the title. This
+ * serves as both a "tooltip" and a place to put buttons.
+ *
+ * Created: Tue Oct 17 13:48:53 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ButtonViewerPopupMenu.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ButtonViewerPopupMenu extends JPopupMenu implements ItemListener
+{
+ private JLabel titleLabel;
+ private GappedSequence currentSequence;
+
+ public ButtonViewerPopupMenu( JAlignmentButtonPanel panel )
+ {
+ add( titleLabel = new JLabel() );
+ addSeparator();
+
+ panel.addItemListener( this );
+ }
+
+ public GappedSequence getSelectedSequence()
+ {
+ return currentSequence;
+ }
+
+ public void itemStateChanged( ItemEvent event )
+ {
+ JAlignmentButtonPanel panel = (JAlignmentButtonPanel)event.getSource();
+ currentSequence = (GappedSequence)event.getItem();
+
+ // (PENDING:- PL) This can be done a lot more simply
+ titleLabel.setText( ((GappedSequence)event.getItem()).getIdentifier().getTitle() );
+
+ // where is the button doing the invoking
+ Point pos = panel.getPointForSequence( currentSequence );
+ // offset it to the edge of the button
+ pos.x += panel.getWidth();
+
+ show( panel, pos.x, pos.y );
+ }
+
+
+} // ButtonViewerPopupMenu
+
+
+
+/*
+ * ChangeLog
+ * $Log: ButtonViewerPopupMenu.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/10/19 17:53:18 lord
+ * Initial checkin. Most of the code has come from CinemaSequenceMenu
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..9a6e405
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/ColorFastAlignmentViewerCellRenderer.java
@@ -0,0 +1,94 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.awt.Graphics;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * ColorFastAlignmentViewerCellRenderer.java
+ *
+ * One of three classes designed to render cells in the
+ * JAlignmentViewer. This one deals specifically with the color of the
+ * cell (background).
+ * <p>
+ * By default, this will drawn first and other things placed on top of
+ * it. However, all this will be determined by the RendererManager.
+ *
+ * Created: Fri Aug 25 14:40:58 2000
+ *
+ * @author Julian Selley
+ * @version $Id: ColorFastAlignmentViewerCellRenderer.java,v 1.5 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ColorFastAlignmentViewerCellRenderer
+ implements FastAlignmentViewerCellRenderer
+{
+ public ColorFastAlignmentViewerCellRenderer() {}
+
+ public void renderAlignmentViewerCell
+ (Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color color,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint)
+ {
+ // draw the background color
+ if ( color != null && element != Gap.GAP ) {
+ g.setColor(color);
+ g.fillRect(x, y, width, height);
+ }
+ }
+} // ColorFastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: ColorFastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/10/03 17:13:20 lord
+ * Now cope with Gap elements correctly
+ *
+ * Revision 1.3 2000/09/21 18:38:49 jns
+ * o fixing a bug - removing the border that it was leaving
+ *
+ * Revision 1.2 2000/09/19 18:08:36 jns
+ * o removal of archiec function that was removed in the interface, and I forgot
+ * to remove it here until now
+ *
+ * Revision 1.1 2000/09/18 17:54:54 jns
+ * o created a new multiplexer cell renderer to take account of cell size
+ * o initial code
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..0061f06
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/CursorLessFastAlignmentViewerCellRenderer.java
@@ -0,0 +1,87 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.Color;
+import java.awt.Graphics;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * CursorLessFastAlignmentViewerCellRenderer.java
+ *
+ *
+ * Created: Thu Jul 13 17:59:36 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CursorLessFastAlignmentViewerCellRenderer.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class CursorLessFastAlignmentViewerCellRenderer
+ extends MultiplexerFastAlignmentViewerCellRenderer
+{
+
+ public CursorLessFastAlignmentViewerCellRenderer(JAlignmentViewer viewer)
+ {
+ super(viewer);
+ }
+
+ public void renderAlignmentViewerCell
+ ( Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color bgColor,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint )
+ {
+ super.renderAlignmentViewerCell
+ ( g, x, y, width, height, viewer, element, location, bgColor, isSelected, hasFocus, false );
+ }
+} // CursorLessFastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: CursorLessFastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/12 13:04:45 jns
+ * o changing renderer to extend the multiplexer with the idea that this
+ * will make the consensus sequence (which uses this renderer) keep pace
+ * with the alignment viewer (which uses the multiplexer) - serving to
+ * keep things more tidy. I have been meaning to do this for ages.
+ *
+ * Revision 1.2 2000/09/18 17:55:42 jns
+ * o change of function name to make more sense
+ *
+ * Revision 1.1 2000/07/18 11:09:01 lord
+ * Import rationalisation.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.java
new file mode 100644
index 0000000..5a076cb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentSelectionRenderer.java
@@ -0,0 +1,71 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import java.awt.Graphics;
+import java.awt.Color;
+
+
+/**
+ * DefaultAlignmentSelectionRenderer.java
+ *
+ *
+ * Created: Wed Mar 7 18:59:56 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultAlignmentSelectionRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultAlignmentSelectionRenderer implements AlignmentSelectionRenderer
+{
+
+ public void renderAlignmentSelection
+ ( Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer,SequenceAlignmentRectangle rect )
+ {
+ g.setColor( Color.black );
+ g.drawRect( x, y, width, height );
+ g.drawRect( x + 1, y + 1, width - 2, height - 2 );
+ g.drawRect( x + 2, y + 2, width - 4, height - 4 );
+ }
+
+} // DefaultAlignmentSelectionRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultAlignmentSelectionRenderer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/03/12 16:34:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..fb318f2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/DefaultAlignmentViewerCellRenderer.java
@@ -0,0 +1,135 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import javax.swing.JLabel;
+import java.awt.Component;
+import uk.ac.man.bioinf.sequence.Element;
+import javax.swing.border.LineBorder;
+import javax.swing.border.Border;
+import javax.swing.border.EmptyBorder;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import java.awt.Color;
+
+
+/**
+ * DefaultAlignmentViewerCellRenderer.java
+ *
+ *
+ * Created: Mon Mar 20 20:23:12 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultAlignmentViewerCellRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultAlignmentViewerCellRenderer extends JLabel implements AlignmentViewerCellRenderer
+{
+ public DefaultAlignmentViewerCellRenderer()
+ {
+
+ }
+ Border green = new LineBorder( Color.green );
+ Border red = new LineBorder( Color.red );
+ Border black = LineBorder.createBlackLineBorder();
+ Border empty = new EmptyBorder( 1, 1, 1, 1 );
+
+ public Component getAlignmentViewerCellRendererComponent
+ ( JAlignmentViewer viewer,
+ Element element,
+ SequenceAlignmentPoint location,
+ Color bgColor,
+ boolean isSelected,
+ boolean cellHasFocus,
+ boolean isAtPoint )
+
+ {
+ if( element != null ){
+ super.setText( "" + element.toChar() );
+ setBorder( black );
+ }
+ else{
+ super.setText( "" );
+ setBorder( empty );
+ }
+
+ if( isSelected ){
+ setBorder( red );
+ }
+
+ if( isAtPoint ){
+ setBorder( green );
+ }
+
+ // set the background color
+ if (bgColor != null) {
+ setOpaque(true);
+ setBackground(bgColor);
+ } else {
+ setOpaque(false);
+ }
+
+ return this;
+ }
+} // DefaultAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultAlignmentViewerCellRenderer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:43:55 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.8 2000/04/13 15:37:39 lord
+ * Cosmetic changes
+ *
+ * Revision 1.7 2000/04/13 15:27:10 lord
+ * Added support for selection colouration
+ *
+ * Revision 1.6 2000/04/12 13:41:28 jns
+ * o added in color mapping code
+ *
+ * Revision 1.5 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.4 2000/03/31 16:21:51 lord
+ * Cosmetic changes
+ *
+ * Revision 1.3 2000/03/29 15:50:47 lord
+ * Updated to use new sequence.geom package
+ *
+ * Revision 1.2 2000/03/21 18:54:21 lord
+ * Now has borders and can cope with null elements
+ *
+ * Revision 1.1 2000/03/21 14:42:08 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..c3c7d95
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/DefaultFastAlignmentViewerCellRenderer.java
@@ -0,0 +1,131 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.Graphics;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+
+
+/**
+ * DefaultFastAlignmentViewerCellRenderer.java
+ *
+ *
+ * Created: Mon Apr 17 20:11:46 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultFastAlignmentViewerCellRenderer.java,v 1.6 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultFastAlignmentViewerCellRenderer implements FastAlignmentViewerCellRenderer
+{
+ public char[] charArray = new char[ 1 ];
+
+ public void renderAlignmentViewerCell
+ ( Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color bgColor,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint )
+ {
+ if( bgColor == null || element == Gap.GAP )
+ bgColor = viewer.getBackground();
+
+ Color borderColor = Color.black;
+
+ if( element != null ){
+
+
+ //draw the contents colour
+ g.setColor( bgColor );
+ g.fillRect( x + 1, y + 1, width - 2, height - 2 );
+
+
+
+ // now draw the char.
+ // (PENDING:- PL) Need to work out the metrics properly.
+ g.setColor( Color.black );
+ FontMetrics mets = g.getFontMetrics();
+ int yOff, xOff;
+ int charWidth = mets.charWidth( element.toChar() );
+ xOff = (width - charWidth ) / 2;
+ yOff = (height + mets.getHeight() - mets.getDescent()) / 2;
+
+ charArray[ 0 ] = element.toChar();
+ g.drawChars( charArray, 0, 1, x + xOff, y + yOff );
+ //if( Debug.debug ) Debug.message( "Drawing cell within " + x + " " + y + " "
+ // + width + " " + height + " .Char is at " + x
+ // + " " + (y + yOff) );
+
+ }
+ else{
+ borderColor = bgColor;
+ g.setColor( viewer.getBackground() );
+ g.fillRect( x, y, width, height );
+ }
+
+ // choose the border colour
+ if( isSelected ){
+ borderColor = Color.red;
+ }
+ if( isAtPoint ){
+ borderColor = Color.green;
+ }
+ //draw the border
+ g.setColor( borderColor );
+ g.drawRect( x, y, width - 1, height - 1 );
+ }
+} // DefaultFastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultFastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.6 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/31 17:54:43 lord
+ * Now draws selection borders even if there is not element.
+ *
+ * Revision 1.4 2000/09/18 17:55:42 jns
+ * o change of function name to make more sense
+ *
+ * Revision 1.3 2000/05/24 15:38:41 lord
+ * Various fiddling. This class is in serious need to a complete rewrite
+ *
+ * Revision 1.2 2000/04/20 14:15:38 lord
+ * Can now cope with null colour map
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.java b/src/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.java
new file mode 100644
index 0000000..778ce1f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/DefaultSequenceCursor.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import uk.ac.man.bioinf.gui.viewer.event.ChangeListenerSupport;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
+
+
+/**
+ * DefaultSequenceCursor.java
+ *
+ *
+ * Created: Tue Apr 4 12:49:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultSequenceCursor.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class DefaultSequenceCursor implements SequenceCursor
+{
+ // listeners
+ private ChangeListenerSupport listenerList = new ChangeListenerSupport();
+
+ // point and mark
+ private SequenceAlignmentPoint point = new SequenceAlignmentPoint();
+ private SequenceAlignmentPoint mark = new SequenceAlignmentPoint();
+
+ public void addChangeListener( ChangeListener listener )
+ {
+ listenerList.addChangeListener( listener );
+ }
+
+ public void removeChangeListener( ChangeListener listener )
+ {
+ listenerList.removeChangeListener( listener );
+ }
+
+ public void setPoint( SequenceAlignmentPoint position )
+ {
+ point = position;
+ listenerList.fireChangeEvent( new ChangeEvent( this ) );
+ }
+
+ public void setMark()
+ {
+ mark = point;
+ listenerList.fireChangeEvent( new ChangeEvent( this ) );
+ }
+
+ public SequenceAlignmentPoint getPoint()
+ {
+ try{
+ return (SequenceAlignmentPoint)point.clone();
+ }
+ catch( CloneNotSupportedException cnse ){
+ return null;
+ }
+ }
+
+ public SequenceAlignmentPoint getMark()
+ {
+ try{
+ return (SequenceAlignmentPoint)mark.clone();
+ }
+ catch( CloneNotSupportedException cnse ){
+ return null;
+ }
+ }
+} // DefaultSequenceCursor
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultSequenceCursor.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/04 14:56:31 lord
+ * Fixed bug with getting Mark
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..82bbeaf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/FastAlignmentViewerCellRenderer.java
@@ -0,0 +1,104 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.Color;
+import java.awt.Graphics;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * FastAlignmentViewerCellRenderer.java
+ *
+ * Although the JAlignmentViewer provides a pluggable renderer
+ * architecture with the AlignmentViewerCellRenderer it has been found
+ * that this has a fairly disasterous effect on performance of the
+ * viewer particularly with respect to scrolling, due to the large
+ * number of method calls and events to render a cell. This class
+ * circumvents all of that, and still provides a degree of
+ * plugability. The disadvantage of using this class is that its much
+ * lower level. You have to do all of the drawing directly onto the
+ * Graphics context provided, and you can not just simply extend a JComponent.
+ *
+ * This interface is the same as for the AlignmentViewerCellRenderer
+ * with the additional information that is required, which is the
+ * graphics context, where to draw on it, and the size to draw.
+ *
+ * Created: Mon Apr 17 20:03:52 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: FastAlignmentViewerCellRenderer.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface FastAlignmentViewerCellRenderer
+{
+ /**
+ * This method renders the cell at the given location in a graphics
+ * object, with reference to the JAlignmentViewer. It makes use of
+ * certain parameters, such as the color of the element being
+ * drawn.
+ *
+ * @param g the graphics object in use
+ * @param x the 'x' location in the graphical display
+ * @param y the 'y' location in the graphical display
+ * @param width the width of the cell
+ * @param height the height of the cell
+ * @param viewer the JAlignmentViewer object
+ * @param element the element being drawn
+ * @param location the sequence alignment location of the element
+ * @param bgColor the background color of the element
+ * @param isSelected whether the element is selected
+ * @param hasFocus whether the element has focus
+ * @param isAtPoint whether the cursor is at the elements point
+ */
+ public void renderAlignmentViewerCell
+ ( Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color bgColor,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint );
+} // FastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: FastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/03/12 16:34:52 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/09/18 17:55:42 jns
+ * o change of function name to make more sense
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/Install.java b/src/uk/ac/man/bioinf/gui/viewer/Install.java
new file mode 100644
index 0000000..eff54e9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/Install.java
@@ -0,0 +1,119 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.UIManager;
+import javax.swing.LookAndFeel;
+import uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI;
+import uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentRulerUI;
+
+
+/**
+ * Install.java
+ *
+ * This class provides the install information for the all of the
+ * classes in the viewer package. It is needed because a Swing
+ * component discovers its UIDelegate by a run time class lookup. The
+ * standard Swing classes get this information from the UIManager
+ * which in turn gets them from the LookAndFeel classes. Since we cant
+ * over ride these this is managed here. At the moment the different
+ * look and feels are not supported (which is to stay that the look
+ * and feel remains the same always!). To get this class to work, just
+ * load it, by calling Install.class.
+ *
+ * Created: Wed Mar 15 17:03:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Install.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class Install implements PropertyChangeListener
+{
+ private static final Install instance = new Install();
+ static
+ {
+ instance.installBasicLookAndFeel();
+ UIManager.addPropertyChangeListener( instance );
+ }
+
+ private LookAndFeel currentLAF;
+
+ public void installBasicLookAndFeel()
+ {
+ // link the JAlignmentViewer to its UIDelegate...
+ UIManager.put( JAlignmentViewer.uiClassID, BasicAlignmentViewerUI.class.getName() );
+ UIManager.put( JAlignmentRuler.uiClassID, BasicAlignmentRulerUI.class.getName() );
+ }
+
+ public void propertyChange( PropertyChangeEvent pce )
+ {
+ if( pce.getPropertyName().equals( "lookAndFeel" ) &&
+ currentLAF != pce.getNewValue() ){
+
+ // currently we are not supporting the different look and feels
+ // as none of the classes here have an equivalent on the
+ // different operating systems. Otherwise we would call
+ // different methods here for the different OS's
+ if( currentLAF == null ){
+ installBasicLookAndFeel();
+ currentLAF = UIManager.getLookAndFeel();
+ }
+ }
+ }
+} // Install
+
+
+
+/*
+ * ChangeLog
+ * $Log: Install.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/18 12:13:05 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.2 2000/03/27 18:49:11 lord
+ * Support for JAlignmentRuler
+ *
+ * Revision 1.1 2000/03/16 16:19:20 lord
+ * Initial checkin
+ *
+ */
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.java b/src/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.java
new file mode 100644
index 0000000..c26915b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/InvertedScrollPaneLayout.java
@@ -0,0 +1,327 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+// (PENDING:- PL) The copyright on this class needs to be modified,
+// because most of the code comes straight from the super class
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import javax.swing.ScrollPaneLayout;
+import java.awt.Container;
+import javax.swing.JScrollPane;
+import java.awt.Rectangle;
+import java.awt.Insets;
+import javax.swing.border.Border;
+import java.awt.Component;
+import java.awt.Dimension;
+import javax.swing.Scrollable;
+
+
+/**
+ * InvertedScrollPaneLayout.java
+ *
+ *
+ * Created: Fri Mar 31 14:27:41 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: InvertedScrollPaneLayout.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class InvertedScrollPaneLayout extends ScrollPaneLayout
+{
+
+ public void layoutContainer( Container parent )
+ {
+ //super.layoutContainer( parent );
+
+ // This code is more or less a straight copy of the super class
+ // method. The bits that I have changed are maked "(PL)" so that I
+ // know what is going on...
+ /* Sync the (now obsolete) policy fields with the
+ * JScrollPane.
+ */
+ JScrollPane scrollPane = (JScrollPane)parent;
+ vsbPolicy = scrollPane.getVerticalScrollBarPolicy();
+ hsbPolicy = scrollPane.getHorizontalScrollBarPolicy();
+
+
+ Rectangle availR = new Rectangle(scrollPane.getSize());
+
+ Insets insets = parent.getInsets();
+ availR.x = insets.left;
+ availR.y = insets.top;
+ availR.width -= insets.left + insets.right;
+ availR.height -= insets.top + insets.bottom;
+
+
+ /* If there's a visible column header remove the space it
+ * needs from the top of availR. The column header is treated
+ * as if it were fixed height, arbitrary width.
+ */
+
+ Rectangle colHeadR = new Rectangle(0, availR.y, 0, 0);
+
+ if ((colHead != null) && (colHead.isVisible())) {
+ int colHeadHeight = colHead.getPreferredSize().height;
+ colHeadR.height = colHeadHeight;
+ // (PL) this line here makes the main view port go to the top of
+ // the scroll pane.
+ //availR.y += colHeadHeight;
+ availR.height -= colHeadHeight;
+ }
+
+ /* If there's a visible row header remove the space it needs
+ * from the left of availR. The row header is treated
+ * as if it were fixed width, arbitrary height.
+ */
+
+ Rectangle rowHeadR = new Rectangle(availR.x, 0, 0, 0);
+
+ if ((rowHead != null) && (rowHead.isVisible())) {
+ int rowHeadWidth = rowHead.getPreferredSize().width;
+ rowHeadR.width = rowHeadWidth;
+ availR.x += rowHeadWidth;
+ availR.width -= rowHeadWidth;
+ }
+
+ /* If there's a JScrollPane.viewportBorder, remove the
+ * space it occupies for availR.
+ */
+
+ Border viewportBorder = scrollPane.getViewportBorder();
+ Insets vpbInsets;
+ if (viewportBorder != null) {
+ vpbInsets = viewportBorder.getBorderInsets(parent);
+ availR.x += vpbInsets.left;
+ availR.y += vpbInsets.top;
+ availR.width -= vpbInsets.left + vpbInsets.right;
+ availR.height -= vpbInsets.top + vpbInsets.bottom;
+ }
+ else {
+ vpbInsets = new Insets(0,0,0,0);
+ }
+
+ colHeadR.x = availR.x;
+ rowHeadR.y = availR.y;
+
+ /* At this point availR is the space available for the viewport
+ * and scrollbars, and the rowHeadR colHeadR rectangles are correct
+ * except for their width and height respectively. Once we're
+ * through computing the dimensions of these three parts we can
+ * go back and set the dimensions of rowHeadR.width, colHeadR.height,
+ * and the bounds for the corners.
+ *
+ * We'll decide about putting up scrollbars by comparing the
+ * viewport views preferred size with the viewports extent
+ * size (generally just its size). Using the preferredSize is
+ * reasonable because layout proceeds top down - so we expect
+ * the viewport to be layed out next. And we assume that the
+ * viewports layout manager will give the view it's preferred
+ * size. One exception to this is when the view implements
+ * Scrollable and Scrollable.getViewTracksViewport{Width,Height}
+ * methods return true. If the view is tracking the viewports
+ * width we don't bother with a horizontal scrollbar, similarly
+ * if view.getViewTracksViewport(Height) is true we don't bother
+ * with a vertical scrollbar.
+ */
+
+ Component view = (viewport != null) ? viewport.getView() : null;
+ Dimension viewPrefSize =
+ (view != null) ? view.getPreferredSize()
+ : new Dimension(0,0);
+
+ Dimension extentSize =
+ (viewport != null) ? viewport.toViewCoordinates(availR.getSize())
+ : new Dimension(0,0);
+
+ boolean viewTracksViewportWidth = false;
+ boolean viewTracksViewportHeight = false;
+ if (view instanceof Scrollable) {
+ Scrollable sv = ((Scrollable)view);
+ viewTracksViewportWidth = sv.getScrollableTracksViewportWidth();
+ viewTracksViewportHeight = sv.getScrollableTracksViewportHeight();
+ }
+
+ /* If there's a vertical scrollbar and we need one, allocate
+ * space for it (we'll make it visible later). A vertical
+ * scrollbar is considered to be fixed width, arbitrary height.
+ */
+
+ Rectangle vsbR = new Rectangle(0, availR.y - vpbInsets.top, 0, 0);
+
+ boolean vsbNeeded;
+ if (vsbPolicy == VERTICAL_SCROLLBAR_ALWAYS) {
+ vsbNeeded = true;
+ }
+ else if (vsbPolicy == VERTICAL_SCROLLBAR_NEVER) {
+ vsbNeeded = false;
+ }
+ else { // vsbPolicy == VERTICAL_SCROLLBAR_AS_NEEDED
+ vsbNeeded = !viewTracksViewportHeight && (viewPrefSize.height > extentSize.height);
+ }
+
+
+ if ((vsb != null) && vsbNeeded) {
+ int vsbWidth = vsb.getPreferredSize().width;
+ availR.width -= vsbWidth;
+ vsbR.x = availR.x + availR.width + vpbInsets.right;
+ vsbR.width = vsbWidth;
+ }
+
+ /* If there's a horizontal scrollbar and we need one, allocate
+ * space for it (we'll make it visible later). A horizontal
+ * scrollbar is considered to be fixed height, arbitrary width.
+ */
+
+ Rectangle hsbR = new Rectangle(availR.x - vpbInsets.left, 0, 0, 0);
+ boolean hsbNeeded;
+ if (hsbPolicy == HORIZONTAL_SCROLLBAR_ALWAYS) {
+ hsbNeeded = true;
+ }
+ else if (hsbPolicy == HORIZONTAL_SCROLLBAR_NEVER) {
+ hsbNeeded = false;
+ }
+ else { // hsbPolicy == HORIZONTAL_SCROLLBAR_AS_NEEDED
+ hsbNeeded = !viewTracksViewportWidth && (viewPrefSize.width > extentSize.width);
+ }
+
+ if ((hsb != null) && hsbNeeded) {
+ int hsbHeight = hsb.getPreferredSize().height;
+ availR.height -= hsbHeight;
+ // (PL) We have to add here the colHead height as well, which is
+ // usually accounted for in the availR.y value...
+ // hsbR.y = availR.y + availR.height + vpbInsets.bottom;
+ hsbR.y = availR.y + availR.height + vpbInsets.bottom + colHeadR.height;
+ hsbR.height = hsbHeight;
+
+ /* If we added the horizontal scrollbar then we've implicitly
+ * reduced the vertical space available to the viewport.
+ * As a consequence we may have to add the vertical scrollbar,
+ * if that hasn't been done so already. Ofcourse we
+ * don't bother with any of this if the vsbPolicy is NEVER.
+ */
+ if ((vsb != null) && !vsbNeeded && (vsbPolicy != VERTICAL_SCROLLBAR_NEVER)) {
+ extentSize = viewport.toViewCoordinates(availR.getSize());
+ vsbNeeded = viewPrefSize.height > extentSize.height;
+
+ if (vsbNeeded) {
+ int vsbWidth = vsb.getPreferredSize().width;
+ availR.width -= vsbWidth;
+ vsbR.x = availR.x + availR.width + vpbInsets.right;
+ vsbR.width = vsbWidth;
+ }
+ }
+ }
+
+ /* We now have the final size of the viewport: availR.
+ * Now fixup the header and scrollbar widths/heights.
+ */
+
+ vsbR.height = availR.height + vpbInsets.top + vpbInsets.bottom;
+ hsbR.width = availR.width + vpbInsets.left + vpbInsets.right;
+ rowHeadR.height = availR.height;
+ colHeadR.width = availR.width;
+
+ // (PL) The column head Y value is not set anywhere as it is
+ // usually the default zero. Change that here. We can ignore the
+ // availR.y value as we know that in this layout manager it is
+ // always going to be zero
+ colHeadR.y = availR.height;
+
+
+ /* Set the bounds of all nine components. The scrollbars
+ * are made invisible if they're not needed.
+ */
+
+ if (viewport != null) {
+ viewport.setBounds(availR);
+ }
+
+ if (rowHead != null) {
+ rowHead.setBounds(rowHeadR);
+ }
+
+ if (colHead != null) {
+ colHead.setBounds(colHeadR);
+ }
+
+ if (vsb != null) {
+ if (vsbNeeded) {
+ vsb.setVisible(true);
+ vsb.setBounds(vsbR);
+ }
+ else {
+ vsb.setVisible(false);
+ }
+ }
+
+ if (hsb != null) {
+ if (hsbNeeded) {
+ hsb.setVisible(true);
+ hsb.setBounds(hsbR);
+ }
+ else {
+ hsb.setVisible(false);
+ }
+ }
+
+ if (lowerLeft != null) {
+ lowerLeft.setBounds(rowHeadR.x, hsbR.y, rowHeadR.width, hsbR.height);
+ }
+
+ if (lowerRight != null) {
+ lowerRight.setBounds(vsbR.x, hsbR.y, vsbR.width, hsbR.height);
+ }
+
+ if (upperLeft != null) {
+ upperLeft.setBounds(rowHeadR.x, colHeadR.y, rowHeadR.width, colHeadR.height);
+ }
+
+ if (upperRight != null) {
+ upperRight.setBounds(vsbR.x, colHeadR.y, vsbR.width, colHeadR.height);
+ }
+ }
+} // InvertedScrollPaneLayout
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvertedScrollPaneLayout.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/05/08 16:29:41 lord
+ * Fiddling whilst Rome burns
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/03/31 16:21:01 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.java b/src/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.java
new file mode 100644
index 0000000..bc08c54
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/JAlignmentButtonPanel.java
@@ -0,0 +1,269 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.AWTEventMulticaster;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.ItemSelectable;
+import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.WeakHashMap;
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+
+
+/**
+ * JAlignmentButtonPanel.java
+ *
+ * This component provides a rank of Buttons relating to a
+ * SequenceAlignment. At the moment it only supports Vertical
+ * alignment. The labels of the buttons are what ever is specified by
+ * the individual Sequence resourceString. These labels define the
+ * width of the overall panel, whilst the height is defined by the
+ * specified height of the individual cells.
+ *
+ * Created: Fri May 19 16:24:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: JAlignmentButtonPanel.java,v 1.8 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class JAlignmentButtonPanel extends JPanel implements ItemSelectable, AlignmentListener
+{
+ private ItemListener itemListener;
+ private int prototypicalCellHeight = 15;
+ private Map buttonMap = new WeakHashMap();
+ private Map colorMap = new WeakHashMap();
+ private SequenceAlignment msa;
+
+ public JAlignmentButtonPanel( )
+ {
+ setLayout( new GridLayout( 0, 1 ) );
+ }
+
+ public JAlignmentButtonPanel( SequenceAlignment msa )
+ {
+ this();
+ setSequenceAlignment( msa );
+ }
+
+ public void setFixedCellHeight( int height )
+ {
+ this.prototypicalCellHeight = height;
+ }
+
+ private Dimension preferredSize = new Dimension();
+ public Dimension getPreferredSize()
+ {
+ // (PENDING:- PL) calculate this properly
+ preferredSize. setSize( 70, getComponentCount() * prototypicalCellHeight );
+ return preferredSize;
+ }
+
+ public Point getPointForSequence( GappedSequence seq )
+ {
+ return ((JButton)buttonMap.get( seq )).getLocation();
+ }
+
+ public void setSequenceColor( GappedSequence seq, Color color )
+ {
+ syncToAlignment();
+ colorMap.put( seq, color );
+ ((JButton)buttonMap.get( seq )).setBackground( color );
+ repaint();
+ }
+
+ public Color getSequenceColor( GappedSequence seq )
+ {
+ return (Color)colorMap.get( seq );
+ }
+
+ public void clearSequenceColor( GappedSequence seq )
+ {
+ setSequenceColor( seq, getBackground() );
+ }
+
+ public void clearAllSequenceColors()
+ {
+ colorMap.clear();
+ syncToAlignment();
+ }
+
+ public void setSequenceAlignment( SequenceAlignment msa )
+ {
+ this.msa = msa;
+ msa.addAlignmentListener( this );
+ syncToAlignment();
+ }
+
+ private void syncToAlignment()
+ {
+ buttonMap.clear();
+ removeAll();
+ // iterate through the msa, and buttons for them all
+ int length = msa.getNumberSequences();
+
+ // set up all the new buttons adding new ones as necessary.
+ for( int i = 0; i < length; i++ ){
+ if( i >= getComponentCount() ){
+ add( new JButton() );
+ }
+
+ GappedSequence seq = msa.getSequenceAt( i + 1);
+ setButton( seq, (JButton)getComponent( i ) );
+ }
+
+ // delete any unnecessary buttons
+ for( int i = getComponentCount(); i > length; i-- ){
+ remove( i );
+ }
+
+ invalidate();
+ repaint();
+ }
+
+ public void setButton( GappedSequence seq, JButton button )
+ {
+ // (PENDING:- PL) Button fonts should inherit straight from the
+ // main component.
+ button.setFont( button.getFont().deriveFont( 6f ) );
+ Color col = (Color)colorMap.get( seq );
+
+ if( col != null ){
+ button.setBackground( col );
+ }
+
+ button.setLabel( seq.getIdentifier().getTitle() );
+ button.addActionListener( new SequenceButtonListener( seq ) );
+ buttonMap.put( seq, button );
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ // (PENDING:- PL) This could be made a lot more restrictive
+ if( event.getType() == AlignmentEventType.DELETE ||
+ event.getType() == AlignmentEventType.INSERT ){
+ syncToAlignment();
+ }
+ }
+
+ public void addItemListener( ItemListener listener )
+ {
+ if( listener == null ) return;
+
+ itemListener = AWTEventMulticaster.add( itemListener, listener );
+ }
+
+ public void removeItemListener( ItemListener listener )
+ {
+ if( listener == null ) return;
+
+ itemListener = AWTEventMulticaster.remove( itemListener, listener );
+ }
+
+ public Object[] getSelectedObjects()
+ {
+ return null;
+ }
+
+ protected void processItemEvent( ItemEvent event )
+ {
+ if( itemListener != null ){
+ itemListener.itemStateChanged( event );
+ }
+ }
+
+ class SequenceButtonListener implements ActionListener
+ {
+ private GappedSequence seq;
+
+ public SequenceButtonListener( GappedSequence seq )
+ {
+ this.seq = seq;
+ }
+
+ public GappedSequence getSequence()
+ {
+ return seq;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ JAlignmentButtonPanel.this.processItemEvent
+ ( new ItemEvent( JAlignmentButtonPanel.this, ItemEvent.ITEM_STATE_CHANGED, seq, ItemEvent.SELECTED ) );
+ }
+ }
+} // JAlignmentButtonPanel
+
+
+
+/*
+ * ChangeLog
+ * $Log: JAlignmentButtonPanel.java,v $
+ * Revision 1.8 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2001/03/12 16:49:29 lord
+ * Moved some code to a new method
+ *
+ * Revision 1.6 2001/03/12 16:36:17 lord
+ * Restricted synchronisation to alignment to when its necessary.
+ *
+ * Revision 1.5 2000/07/18 11:09:14 lord
+ * Changes due to removal of biointerface
+ *
+ * Revision 1.4 2000/06/27 16:00:23 lord
+ * Added getPointForSequence information which makes PopupMenu placement
+ * a lot easier.
+ * Now listens to the alignment and responds when a new sequence is added
+ *
+ * Revision 1.3 2000/06/05 14:23:14 lord
+ * Fixed bug. The last sequence in the alignment was not getting shown.
+ *
+ * Revision 1.2 2000/05/30 16:22:55 lord
+ * Changed some method names
+ *
+ * Revision 1.1 2000/05/24 15:39:05 lord
+ * Initial checkin
+ *
+ */
+
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.java b/src/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.java
new file mode 100644
index 0000000..cad39cf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/JAlignmentRuler.java
@@ -0,0 +1,248 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import javax.swing.JSlider;
+import javax.swing.plaf.SliderUI;
+import javax.swing.UIManager;
+import java.awt.Dimension;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import javax.swing.DefaultBoundedRangeModel;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment;
+
+
+/**
+ * JAlignmentRuler.java
+ *
+ *
+ *
+ * Created: Thu Mar 23 12:33:50 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: JAlignmentRuler.java,v 1.6 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class JAlignmentRuler extends JSlider
+{
+ public static final String uiClassID = "AlignmentRulerUI";
+ private int widthPerBase;
+ protected int preferredHeight = 50;
+ private SequenceAlignment seq;
+
+ public JAlignmentRuler()
+ {
+ this( EmptySequenceAlignment.getInstance() );
+ }
+
+ public JAlignmentRuler( SequenceAlignment seq )
+ {
+ this( seq, JSlider.HORIZONTAL );
+ }
+
+ public JAlignmentRuler( SequenceAlignment seq, int orientation )
+ {
+ this( seq, orientation, 1 );
+ }
+
+ public JAlignmentRuler( SequenceAlignment seq, int orientation, int widthPerBase )
+ {
+ super();
+ this.seq = seq;
+ setModel( new SequenceAlignmentBoundRangeModelBridge( seq ) );
+ setOrientation( orientation );
+ calcDefaultLabelTable();
+ }
+
+ public void setSequenceAlignment( SequenceAlignment msa )
+ {
+ seq = msa;
+ setModel( new SequenceAlignmentBoundRangeModelBridge( msa ) );
+ calcDefaultLabelTable();
+ firePropertyChange( "sequenceAlignment", msa, seq );
+ }
+
+ private void calcDefaultLabelTable()
+ {
+ setMinorTickSpacing(2);
+ setMajorTickSpacing(10);
+ setPaintTicks(true);
+ setPaintLabels(true);
+ setLabelTable(createStandardLabels(10));
+ }
+
+ public SequenceAlignment getSequenceAlignment()
+ {
+ return seq;
+ }
+
+ public Dimension getMinimumSize()
+ {
+ return getPreferredSize();
+ }
+
+ public Dimension getMaximumSize()
+ {
+ return getPreferredSize();
+ }
+
+ public int getPreferredHeight()
+ {
+ return preferredHeight;
+ }
+
+ public int getPreferredWidthPerBase()
+ {
+ return widthPerBase;
+ }
+
+ public void setPreferredWidthPerBase( int widthPerBase )
+ {
+ this.widthPerBase = widthPerBase;
+ }
+
+ public String getUIClassID()
+ {
+ return uiClassID;
+ }
+
+ public void setUI( SliderUI ui )
+ {
+ super.setUI( ui );
+ }
+
+ public void updateUI()
+ {
+ setUI( (SliderUI)UIManager.getUI( this ) );
+ }
+
+ class SequenceAlignmentBoundRangeModelBridge
+ extends DefaultBoundedRangeModel implements AlignmentListener
+
+ {
+ private SequenceAlignment seq;
+
+ public SequenceAlignmentBoundRangeModelBridge( SequenceAlignment seq )
+ {
+ this( seq, 1, 0 );
+ }
+
+ public SequenceAlignmentBoundRangeModelBridge( SequenceAlignment seq, int value, int extent )
+ {
+ // set the values of the super class. Starts at 1, ends at one
+ // plus length
+ super( value, extent, 1, seq.getLength() + 1 );
+ this.seq = seq;
+ seq.addAlignmentListener( this );
+ }
+
+ public SequenceAlignment getSequenceAlignment()
+ {
+ return seq;
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ // (PENDING:- PL) This can be changed to check for specific
+ // events and only signal when necessary.
+ super.setRangeProperties( 1, 0, 1, seq.getLength(), false );
+ calcDefaultLabelTable();
+ }
+
+ public void setRangeProperties( int a, int b, int c, int d, boolean adjusting )
+ {
+ // I really really hate to do this but.
+ if( c != SequenceAlignmentBoundRangeModelBridge.this.getMinimum() ||
+ d != SequenceAlignmentBoundRangeModelBridge.this.getMaximum() ){
+ throw new RuntimeException( "You reset the min and max of this model. Its fixed for ever and a day.");
+ }
+ }
+
+ public void setMinimum( int a )
+ {
+ // I really really hate to do this but.
+ throw new RuntimeException( "You reset the min of this model. Its fixed for ever and a day.");
+ }
+
+ public void setMaximum( int b )
+ {
+ // I really really hate to do this but.
+ throw new RuntimeException( "You reset the max of this model. Its fixed for ever and a day.");
+ }
+
+ }
+
+ static
+ {
+ // ensure that UI delegates are known to swing
+ Class c = Install.class;
+ }
+} // JAlignmentRuler
+
+
+
+/*
+ * ChangeLog
+ * $Log: JAlignmentRuler.java,v $
+ * Revision 1.6 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/07/18 11:09:25 lord
+ * Import rationalisation.
+ *
+ * Revision 1.4 2000/06/27 16:01:49 lord
+ * Fixed bug in the event handling so that this class does really listen
+ * to the alignment now.
+ *
+ * Revision 1.3 2000/04/20 14:17:05 lord
+ * Fixed bug in model constructor.
+ * Moved tick calculation to private method, as these need to be called
+ * on resetting the MSA
+ *
+ * Revision 1.2 2000/04/19 17:21:06 lord
+ * Put in default cons, put in standard tick marks, and added load of
+ * install class
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.4 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.3 2000/04/03 13:52:48 lord
+ * Fixed bug with upper limit of model being one too small
+ *
+ * Revision 1.2 2000/03/29 14:52:42 lord
+ * Now calculates preferred size. Has a preferred width per base
+ * option.
+ *
+ * Revision 1.1 2000/03/27 18:59:04 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.java b/src/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.java
new file mode 100644
index 0000000..87a8ca7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/JAlignmentViewer.java
@@ -0,0 +1,900 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.Dimension;
+import java.awt.Point;
+import java.awt.Rectangle;
+import javax.swing.JComponent;
+import javax.swing.SwingConstants;
+import javax.swing.UIManager;
+import javax.swing.event.ChangeListener;
+import uk.ac.man.bioinf.gui.color.ColorMap;
+import uk.ac.man.bioinf.gui.color.SingleColorMap;
+import uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer;
+import uk.ac.man.bioinf.gui.viewer.plaf.AlignmentViewerUI;
+import uk.ac.man.bioinf.sequence.alignment.EmptySequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent;
+
+
+
+/**
+ * JAlignmentViewer.java
+ *
+ *
+ * Created: Tue Mar 14 16:28:59 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: JAlignmentViewer.java,v 1.28 2002/03/08 14:53:57 lord Exp $
+ */
+
+public class JAlignmentViewer extends JComponent
+ implements AlignmentListener, SequenceListener, AlignmentSelectionListener //,Scrollable
+{
+ public static final String uiClassID = "AlignmentViewerUI";
+ private SequenceAlignment alignment;
+ // (PENDING:- PL) this default is not really acceptable. It should be
+ // changed to something more sensible, using the preferred size of
+ // the CellRenderer
+ private Dimension prototypicalCellSize = new Dimension( 30, 30 );
+ private AlignmentViewerCellRenderer renderer;
+ private FastAlignmentViewerCellRenderer fastRenderer =
+ new DefaultFastAlignmentViewerCellRenderer();
+ private AlignmentSelectionRenderer selectionRenderer =
+ new DefaultAlignmentSelectionRenderer();
+ private SequenceCursor cursor;
+ private AlignmentViewerUI viewerUI;
+ private AlignmentSelectionModel selectionModel;
+ private ColorMap colorMap;
+
+ public JAlignmentViewer()
+ {
+ this( EmptySequenceAlignment.getInstance() );
+ }
+
+ public JAlignmentViewer( SequenceAlignment alignment )
+ {
+ super();
+ // (PENDING:- PL) We probably need to install listeners here to
+ // this SequenceAlignment. Should we allow it to change outside? I
+ // think so...
+ this.alignment = alignment;
+ cursor = new DefaultSequenceCursor();
+ colorMap = new SingleColorMap(getBackground());
+
+ selectionModel = new SingleAlignmentSelectionModel();
+ selectionModel.addAlignmentSelectionListener( this );
+ // bit surprising here, but this is NOT called by the super class cons
+ updateUI();
+ }
+
+ // rendering properties
+ public void setCellRenderer( AlignmentViewerCellRenderer renderer )
+ {
+ AlignmentViewerCellRenderer old = this.renderer;
+ this.renderer = renderer;
+ firePropertyChange( "cellRenderer", old, renderer );
+ }
+
+ public AlignmentViewerCellRenderer getCellRenderer()
+ {
+ return renderer;
+ }
+
+ public void setFastCellRenderer( FastAlignmentViewerCellRenderer renderer )
+ {
+ FastAlignmentViewerCellRenderer old = this.fastRenderer;
+ this.fastRenderer = renderer;
+ firePropertyChange("fastCellRenderer", old, renderer);
+ }
+
+ public FastAlignmentViewerCellRenderer getFastCellRenderer()
+ {
+ return fastRenderer;
+ }
+
+ public void setAlignmentSelectionRenderer( AlignmentSelectionRenderer selectionRenderer )
+ {
+ AlignmentSelectionRenderer old = this.selectionRenderer;
+ this.selectionRenderer = selectionRenderer;
+ firePropertyChange( "alignmentSelectionRenderer", old, selectionRenderer );
+ }
+
+ public AlignmentSelectionRenderer getAlignmentSelectionRenderer()
+ {
+ return selectionRenderer;
+ }
+
+ public void setCellHeight( int height )
+ {
+ int old = prototypicalCellSize.height;
+ prototypicalCellSize.height = height;
+
+ firePropertyChange( "cellHeight", old, height );
+ }
+
+ public int getCellHeight()
+ {
+ return prototypicalCellSize.height;
+ }
+
+ public void setCellWidth( int width )
+ {
+ int old = prototypicalCellSize.width;
+ prototypicalCellSize.width = width;
+ firePropertyChange( "cellWidth", old, width );
+ }
+
+ public int getCellWidth()
+ {
+ return prototypicalCellSize.width;
+ }
+
+
+ // sizing methods
+ private Dimension preferredSize = new Dimension( 0, 0 );
+ public Dimension getPreferredSize()
+ {
+ // (PENDING:- PL) This does not need to be necessarily need to
+ // recalculated every time.
+ preferredSize.setSize
+ // (PENDING:- PL) Have to put in code to account of Ruler
+ // size. Delegate this to UI??
+
+ // Leave a little gap at the edge here so that we can see all of
+ // the elements
+ ( alignment.getLength() * getCellWidth(),
+ alignment.getNumberSequences() * getCellHeight() );
+
+ // return preferredSize;
+ return preferredSize;
+ }
+
+ public Dimension getMinimumSize()
+ {
+ return getPreferredSize();
+ }
+
+ public Dimension getMaximumSize()
+ {
+ return getPreferredSize();
+ }
+
+ // color methods and delegates
+ /**
+ * Changes the color map and notifies of change.
+ *
+ * @param colorMap the new color map
+ */
+ public void setColorMap(ColorMap colorMap)
+ {
+ if( colorMap == null ) colorMap = new SingleColorMap( getBackground() );
+
+ ColorMap old = this.colorMap;
+ this.colorMap = colorMap;
+ firePropertyChange( "colorMap", old, colorMap);
+ repaint();
+ }
+
+ /**
+ * Returns the current color map.
+ *
+ * @return the color map
+ */
+ public ColorMap getColorMap()
+ {
+ return this.colorMap;
+ }
+
+ // cursor methods and delegates
+ public void setCursorModel( SequenceCursor cursor )
+ {
+ SequenceCursor old = this.cursor;
+ this.cursor = cursor;
+ firePropertyChange( "sequenceCursor", old, cursor );
+ }
+
+ public SequenceCursor getCursorModel()
+ {
+ return cursor;
+ }
+
+ public void addCursorChangeListener( ChangeListener listener )
+ {
+ cursor.addChangeListener( listener );
+ }
+
+ public void removeCursorChangeListener( ChangeListener listener )
+ {
+ cursor.removeChangeListener( listener );
+ }
+
+ public void setPoint( SequenceAlignmentPoint point )
+ {
+ // (PENDING:- PL) Need to think clearly about what to in the case
+ // that this goes out of bounds...
+ if( point.getX() < 1 || point.getY() < 1 ||
+ point.getX() > alignment.getLength() ||
+ point.getY() > alignment.getNumberSequences() )
+ return;
+
+ SequenceAlignmentPoint oldPoint = cursor.getPoint();
+ cursor.setPoint( point );
+ ensureSequencePointIsVisible( point );
+ repaint( getCellBounds( oldPoint ) );
+ repaint( getCellBounds( point ) );
+ }
+
+ public void setMark()
+ {
+ cursor.setMark();
+ }
+
+ public void moveCursor(SequenceAlignmentPoint newPoint)
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move(newPoint.getX(), newPoint.getY()));
+ }
+
+ public void moveCursorUp( int number )
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint
+ ( point.move
+ ( point.getX(), point.getY() - number ) );
+ }
+
+ public void moveCursorDown( int number )
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint
+ ( point.move
+ ( point.getX(), point.getY() + number ) );
+ }
+
+ public void moveCursorPageUp()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ if ((point.getY() -
+ (getVisibleSequenceRectangle().getSize().getHeight() - 2)) < 1)
+ setPoint(point.move(point.getX(), 1));
+ else
+ setPoint(point.move
+ (point.getX(), point.getY() -
+ (getVisibleSequenceRectangle().getSize().getHeight() - 2)));
+ }
+
+ public void moveCursorPageDown()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ if ((point.getY() +
+ (getVisibleSequenceRectangle().getSize().getHeight() - 2)) < 1)
+ setPoint(point.move(point.getX(), alignment.getNumberSequences()));
+ else
+ setPoint(point.move
+ (point.getX(), point.getY() +
+ (getVisibleSequenceRectangle().getSize().getHeight() - 2)));
+ }
+
+ public void moveCursorBeginningOfAlignment()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move(1,1));
+ }
+
+ public void moveCursorEndOfAlignment()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move
+ (alignment.getSequenceAt(alignment.getNumberSequences()).getGappedLength(),
+ alignment.getNumberSequences()));
+ }
+
+ public void moveCursorRight( int number )
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint
+ ( point.move
+ ( point.getX() + number, point.getY() ) );
+ }
+
+ public void moveCursorLeft( int number )
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint
+ ( point.move
+ ( point.getX() - number, point.getY() ) );
+ }
+
+ public void moveCursorPageRight()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move
+ (point.getX() +
+ (getVisibleSequenceRectangle().getSize().getWidth() - 2),
+ point.getY()));
+ }
+
+ public void moveCursorPageLeft()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move
+ (point.getX() -
+ (getVisibleSequenceRectangle().getSize().getWidth() - 2),
+ point.getY()));
+ }
+
+ public void moveCursorBeginningOfSequence()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move(1, point.getY()));
+ }
+
+ public void moveCursorEndOfSequence()
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move
+ ((alignment.getSequenceAt(point.getY()).getGappedLength() +
+ alignment.getInset(point.getY())), point.getY()));
+ }
+
+ public void moveCursorToSequencePoint(int x, int y)
+ {
+ SequenceAlignmentPoint point = cursor.getPoint();
+ setPoint(point.move(x, y));
+ ensureSequencePointIsVisible(point);
+ }
+
+ public void moveCursorToSequencePoint( SequenceAlignmentPoint point )
+ {
+ moveCursorToSequencePoint( point.getX(), point.getY() );
+ }
+
+ public SequenceAlignmentPoint getPoint()
+ {
+ return cursor.getPoint();
+ }
+
+ public SequenceAlignmentPoint getMark()
+ {
+ return cursor.getMark();
+ }
+
+ // methods delegated to UI
+ public SequenceAlignmentPoint getSequencePointAtPoint( int x, int y )
+ {
+ return viewerUI.getSequencePointAtPoint( x, y );
+ }
+
+ public SequenceAlignmentPoint getSequencePointAtPoint( Point point )
+ {
+ return getSequencePointAtPoint
+ ( point.x, point.y );
+ }
+
+ public Point getPointAtSequencePoint( int x, int y )
+ {
+ return viewerUI.getPointAtSequencePoint( x, y );
+ }
+
+ private Rectangle cacheRect;
+ public Rectangle getRectangleForSequenceRectangle( SequenceAlignmentRectangle seqRect )
+ {
+ if( cacheRect == null ) cacheRect = new Rectangle();
+
+ cacheRect.setLocation( getPointAtSequencePoint( seqRect.getX(), seqRect.getY() ) );
+ cacheRect.setSize
+ ( (seqRect.getWidth()) * getCellWidth(), (seqRect.getHeight()) * getCellHeight() );
+ return cacheRect;
+ }
+
+ public Rectangle getCellBounds( SequenceAlignmentPoint point )
+ {
+ return viewerUI.getCellBounds( point );
+ }
+
+ public void ensureSequencePointIsVisible( SequenceAlignmentPoint point )
+ {
+ scrollRectToVisible
+ ( getCellBounds( point ) );
+ }
+
+ // is the alignment viewer read-only
+ protected boolean readonly = false;
+ public void setReadonly(boolean readonly)
+ {
+ if (this.readonly != readonly) {
+ this.readonly = readonly;
+ firePropertyChange("readonly", !readonly, readonly);
+ }
+ }
+
+ public boolean isReadonly()
+ {
+ return this.readonly;
+ }
+
+ public void insertGapsAt(SequenceAlignmentPoint point, int sizeOfGap)
+ throws SequenceVetoException, AlignmentVetoException, ReadonlyException
+ {
+ // check whether the viewer is readonly at the moment
+ if (isReadonly())
+ throw new ReadonlyException(this);
+
+ // if the point is beyond the sequence length then return
+ if ((point.getX() - alignment.getInset(point.getY())) >
+ alignment.getSequenceAt(point.getY()).getGappedLength())
+ return;
+
+ // insert the gaps if in a sequence
+ if ((point.getX() - alignment.getInset(point.getY())) > 1)
+ // insert the gaps - this is where the veto might come from
+ alignment.getSequenceAt(point.getY()).insertGapAt
+ (point.getX() - alignment.getInset(point.getY()), sizeOfGap);
+ else
+ // otherwise extend the inset of the sequence
+ alignment.setInset(point.getY(),
+ (alignment.getInset(point.getY()) + sizeOfGap));
+ }
+
+ public void insertGapsAt(int x, int y, int sizeOfGap)
+ throws SequenceVetoException, AlignmentVetoException, ReadonlyException
+ {
+ // delegate function
+ this.insertGapsAt(new SequenceAlignmentPoint(x, y), sizeOfGap);
+ }
+
+ public void deleteGapsAt(SequenceAlignmentPoint point, int sizeOfGap)
+ throws NoGapAtThisPositionException, SequenceVetoException,
+ AlignmentVetoException, ReadonlyException
+ {
+ // check whether alignment is read-only
+ if (isReadonly())
+ throw new ReadonlyException(this);
+
+ // if the point is beyond the sequence length then return
+ if ((point.getX() - alignment.getInset(point.getY())) >
+ alignment.getSequenceAt(point.getY()).getGappedLength())
+ return;
+
+ // try to remove the gaps
+ if ((point.getX() - alignment.getInset(point.getY())) > 0)
+ // remove the gaps if in the sequence
+ alignment.getSequenceAt(point.getY()).deleteGapAt
+ (point.getX() - alignment.getInset(point.getY()), sizeOfGap);
+ else
+ // otherwise decrease the inset
+ alignment.setInset(point.getY(),
+ (alignment.getInset(point.getY()) - sizeOfGap));
+
+ // calculate the screen location of the cursor
+ Point screenPoint = getPointAtSequencePoint(point.getX(), point.getY());
+ Rectangle viewerSize = this.getBounds();
+ }
+
+ public void deleteGapsAt(int x, int y, int sizeOfGap)
+ throws NoGapAtThisPositionException, SequenceVetoException,
+ AlignmentVetoException, ReadonlyException
+ {
+ // delegate function
+ this.deleteGapsAt(new SequenceAlignmentPoint(x, y), sizeOfGap);
+ }
+
+ public void insertGapsAtCursor(int sizeOfGap)
+ throws SequenceVetoException, AlignmentVetoException, ReadonlyException
+ {
+ // get the cursor location to remove gaps at this point
+ SequenceAlignmentPoint point = getPoint();
+
+ // delegate function
+ this.insertGapsAt(point, sizeOfGap);
+
+ // move the cursor right, so that remain with insertion point
+ moveCursorRight(sizeOfGap);
+ }
+
+ public void deleteGapsAtCursor(int sizeOfGap)
+ throws NoGapAtThisPositionException, SequenceVetoException,
+ AlignmentVetoException, ReadonlyException
+ {
+ // get the cursor location to remove gaps at this point
+ SequenceAlignmentPoint point = getPoint();
+
+ // delegate function
+ this.deleteGapsAt(point, sizeOfGap);
+ }
+
+ public SequenceAlignmentRectangle getVisibleSequenceRectangle()
+ {
+ Rectangle rect = getVisibleRect();
+ SequenceAlignmentRectangle seqRect = new SequenceAlignmentRectangle();
+ seqRect.setLocation
+ ( getSequencePointAtPoint( rect.x, rect.y ) );
+ // we need to remember the sequence point before the resize
+
+ seqRect.add( getSequencePointAtPoint( rect.x + rect.height, rect.y + rect.width ) );
+
+ return seqRect;
+ }
+
+ // selection model methods
+ public AlignmentSelectionModel getSelectionModel()
+ {
+ return selectionModel;
+ }
+
+ public void setSelectionModel( AlignmentSelectionModel selectionModel )
+ {
+ AlignmentSelectionModel old = this.selectionModel;
+ this.selectionModel = selectionModel;
+ old.removeAlignmentSelectionListener( this );
+ selectionModel.addAlignmentSelectionListener( this );
+ firePropertyChange( "alignmentSelectionModel", old, selectionModel );
+ repaint();
+ }
+
+ public void extendSelection( SequenceAlignmentPoint point )
+ {
+ selectionModel.extendSelection( point );
+ }
+
+ public void stopSelection( SequenceAlignmentPoint point )
+ {
+ selectionModel.stopSelection( point );
+ }
+
+ public void clearSelection()
+ {
+ selectionModel.clearSelection();
+ }
+
+ // get data models
+ public void setSequenceAlignment( SequenceAlignment msa )
+ {
+ SequenceAlignment old = alignment;
+ alignment = msa;
+
+ // sort out listeners. We need those so we can redraw in response
+ // to events
+ alignment.addSequenceListener( this );
+ alignment.addAlignmentListener( this );
+
+ old.removeSequenceListener( this );
+ old.removeAlignmentListener( this );
+
+ // reset cursor and selection (PENDING:- PL) Colour map as well?
+ setPoint( new SequenceAlignmentPoint() );
+ setMark();
+ clearSelection();
+
+ firePropertyChange( "sequenceAlignment", old, alignment );
+ // make sure that the appearance of the GUI reflects the change!
+ invalidate();
+ repaint();
+ }
+
+ public SequenceAlignment getSequenceAlignment()
+ {
+ return alignment;
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ // SequenceAlignmentRectangle visRect = getVisibleSequenceRect();
+
+ // int start = event.getStart();
+ // int end = event.getEnd();
+
+ // // if any of the affected rows are visible redraw
+ // if( (start > visRect.getX() && start < visRect.getX() + visRect.getWidth()) ||
+ // (end > visRect.getX() && end < visRect.getX() + visRect.getWidth() ) ){
+ // repaint();
+ // }
+
+ // changed my mind. By the time we have done all the stuff above
+ // we might as well just repaint()!
+ repaint();
+ }
+
+ private Rectangle viewerRect = null;
+ public void changeOccurred( SequenceEvent event )
+ {
+ // get the bounds of the viewer and store for later use
+ // this uses one object for speed optimization
+ viewerRect = getBounds(viewerRect);
+ // get the source of the event - this should be a gapped sequence
+ // but this may be where my brilliant coding falls down
+ GappedSequence src = (GappedSequence)event.getSource();
+ // get the screen point of the location of the event
+ Point srcScreenPoint = getPointAtSequencePoint
+ (event.getStart() - event.getLength(),
+ alignment.getSequenceIndex(src));
+
+ // before repaint did the event occur in the visible area?
+ if (viewerRect.contains(srcScreenPoint)) {
+ // repaint from the event to the right *only* in the sequence
+ // where the event occurred
+ repaint(new Rectangle(srcScreenPoint.x, srcScreenPoint.y,
+ viewerRect.width - srcScreenPoint.x,
+ getCellHeight()));
+ } else {
+ // if I have messed up my calculations, we may need to put this
+ // back in, but for now this won't do anything.
+ //repaint();
+ }
+ }
+
+ private SequenceAlignmentRectangle previousSelection;
+
+ public void valueChanged( AlignmentSelectionEvent event )
+ {
+ if( event.getSelectionRectangle() != null ){
+ if( previousSelection != null ){
+ repaint( getRectangleForSequenceRectangle( previousSelection ) );
+ }
+
+ // repaint the region, and store the region for next time. Make
+ // this a clone to ensure that its not changed behind our back
+ repaint
+ ( getRectangleForSequenceRectangle
+ ( previousSelection = new SequenceAlignmentRectangle( event.getSelectionRectangle() ) ) );
+
+ }
+ }
+
+
+ // Scrollable interface
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ return getPreferredSize();
+ }
+
+ public int getScrollableUnitIncrement( Rectangle visibleRect, int orientation, int direction )
+ {
+ if( orientation == SwingConstants.HORIZONTAL ){
+ if( direction > 0 ){
+ // scrolling right.
+ SequenceAlignmentPoint seqPoint = getSequencePointAtPoint( visibleRect.x, visibleRect.y );
+ Rectangle rect = getCellBounds( seqPoint );
+
+ int inc = visibleRect.x - rect.x;
+ return inc;
+ }
+ }
+ return 0;
+
+ }
+
+ public int getScrollableBlockIncrement( Rectangle visibleRect, int orientation, int direction )
+ {
+ return 0;
+ }
+
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return false;
+ }
+
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
+
+
+ // these methods tie the this class into its equivalent UI
+ // delegate.
+ public String getUIClassID()
+ {
+ return uiClassID;
+ }
+
+ public void setUI( AlignmentViewerUI ui )
+ {
+ super.setUI( ui );
+ viewerUI = (AlignmentViewerUI)ui;
+ }
+
+ public void updateUI()
+ {
+ setUI( (AlignmentViewerUI)UIManager.getUI( this ) );
+ }
+
+ static
+ {
+ // ensure that UI delegates are known to swing.
+ Class c = Install.class;
+ }
+
+} // JAlignmentViewer
+
+
+
+/*
+ * ChangeLog
+ * $Log: JAlignmentViewer.java,v $
+ * Revision 1.28 2002/03/08 14:53:57 lord
+ * Cosmetic changes
+ *
+ * Revision 1.27 2001/05/22 15:50:53 lord
+ * New convenience method
+ *
+ * Revision 1.26 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.25 2001/03/12 16:34:12 lord
+ * Alignment selection renderer added
+ *
+ * Revision 1.24 2001/01/22 14:59:30 lord
+ * Fixed repaint bug on selection
+ *
+ * Revision 1.23 2001/01/19 19:54:02 lord
+ * Updated due to changes in SequenceAlignmentRectangle
+ *
+ * Revision 1.22 2001/01/15 18:55:13 lord
+ * Improvement to selection model handling.
+ *
+ * Revision 1.21 2001/01/04 14:58:40 lord
+ * Sorted imports
+ *
+ * Revision 1.20 2001/01/04 14:26:13 jns
+ * o Bug fixing: had moved ReadonlyException to a new location, but
+ * forgot to deal with the package statements, etc.
+ *
+ * Revision 1.19 2000/12/20 16:44:10 jns
+ * o added in a read-only attribute and got the insertion and deletion of
+ * gaps to check this. This was added in so that the viewer can be made
+ * readonly.
+ *
+ * o bug-fix: I had done something weird with the rectangle repaint -
+ * don't ask me what I was on. Anyway, hopefully I have sorted the
+ * problem and it now paints from the x,y to the edge of the viewer and
+ * the height of one sequence.
+ *
+ * o removed some System.out's to reduce the amount of stuff being sent
+ * to STDOUT - these ought to be either STDERR or debug statements. As
+ * far as I could see, the comments I have removed are irrelevant stuff.
+ *
+ * Revision 1.18 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.17 2000/12/05 14:54:20 lord
+ * Documentation update
+ *
+ * Revision 1.16 2000/11/02 14:49:53 jns
+ * o added insert and delete gaps at a specific location, rather than
+ * relying on the cursor to be in the correct place.
+ *
+ * Revision 1.15 2000/10/31 13:22:21 jns
+ * o re-did the repaint on changeOccurred (SequenceEvent event). It now
+ * repaints the correct bit - hopefully
+ *
+ * Revision 1.14 2000/10/26 17:21:27 jns
+ * o added mouse click to move cursor
+ *
+ * Revision 1.13 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.12 2000/09/27 16:18:12 jns
+ * o added various methods to move the cursor around the
+ * alignment. Hopefully this will help with cursor movement around the
+ * alignment.
+ * o reverted back to single fast cell renderer, because of the ability
+ * to generate a multiplexer cell renderer that will render multiple cell
+ * renderers at one time.
+ *
+ * Revision 1.11 2000/09/18 17:58:52 jns
+ * o change to support multiple renderers, in preparation for the multiplexer
+ * cell renderer which uses three cell renderers to render a cell
+ *
+ * Revision 1.10 2000/08/01 17:12:24 lord
+ * Cosmetic
+ *
+ * Revision 1.9 2000/07/18 11:09:33 lord
+ * Import rationalisation.
+ *
+ * Revision 1.8 2000/06/27 16:03:30 lord
+ * Small fix. Now no longer leaves a gap at the bottom of the component.
+ * This means that I can use it as a single sequence viewer sensibly.
+ *
+ * Revision 1.7 2000/06/13 11:12:49 lord
+ * Added more event support
+ *
+ * Revision 1.6 2000/06/05 14:23:30 lord
+ * Cosmetic changes
+ *
+ * Revision 1.5 2000/05/30 16:23:14 lord
+ * Can now cope with colour map == null
+ *
+ * Revision 1.4 2000/05/24 15:39:51 lord
+ * Sorted imports
+ * Bad (non working) implementation of Scrollable interface
+ *
+ * Revision 1.3 2000/04/20 14:17:54 lord
+ * Can now reset MSA
+ *
+ * Revision 1.2 2000/04/19 17:21:32 lord
+ * Default constructor added, and ensure Install class loaded
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.12 2000/04/18 17:32:01 lord
+ * Modified to take Fast renderer as well as normal one
+ *
+ * Revision 1.11 2000/04/13 12:42:26 lord
+ * Added support for selection
+ *
+ * Revision 1.10 2000/04/12 13:41:36 jns
+ * o added in color mapping code
+ *
+ * Revision 1.9 2000/04/11 17:17:35 lord
+ * Elementary selection support added. Probably buggy at the moment
+ *
+ * Revision 1.8 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.7 2000/04/03 13:54:18 lord
+ * Removed references to ruler
+ * Fixed bug in size calculations
+ *
+ * Revision 1.6 2000/03/31 16:23:35 lord
+ * Removed JAlignmentRuler references as this is now done instead by the
+ * JScrollPane
+ *
+ * Revision 1.5 2000/03/29 14:54:48 lord
+ * Moved some of the slider set up stuff into the "setJAlignmentRuler"
+ * method. Also made the changes necessary to cope with preferred size of
+ * the ruler
+ *
+ * Revision 1.4 2000/03/27 18:49:55 lord
+ * Preliminary addition of SequenceRuler and support methods
+ *
+ * Revision 1.3 2000/03/21 18:53:23 lord
+ * Removed system out's
+ *
+ * Revision 1.2 2000/03/21 13:41:35 lord
+ * Have basic system up now. Installs UI, uses renderer etc
+ *
+ * Revision 1.1 2000/03/16 16:19:20 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.java b/src/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.java
new file mode 100644
index 0000000..b0be727
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/JChangedScrollPane.java
@@ -0,0 +1,83 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import javax.swing.JScrollPane;
+import java.awt.Component;
+import javax.swing.ScrollPaneLayout;
+
+
+/**
+ * JChangedScrollPane.java
+ *
+ *
+ * Created: Fri Mar 31 14:56:45 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: JChangedScrollPane.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class JChangedScrollPane extends JScrollPane
+{
+
+ public JChangedScrollPane( Component view, int vsbPolicy, int hsbPolicy )
+ {
+ this( new ScrollPaneLayout.UIResource(), view, vsbPolicy, hsbPolicy );
+ }
+
+ public JChangedScrollPane( ScrollPaneLayout layout, Component view, int vsbPolicy, int hsbPolicy )
+ {
+ setLayout( layout );
+ setVerticalScrollBarPolicy(vsbPolicy);
+ setHorizontalScrollBarPolicy(hsbPolicy);
+ setViewport(createViewport());
+ setVerticalScrollBar(createVerticalScrollBar());
+ setHorizontalScrollBar(createHorizontalScrollBar());
+ if ( view != null) {
+ setViewportView(view);
+ }
+ updateUI();
+ }
+
+} // JChangedScrollPane
+
+
+
+/*
+ * ChangeLog
+ * $Log: JChangedScrollPane.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/03/31 16:21:01 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.java b/src/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.java
new file mode 100644
index 0000000..79ce3f8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/JLayableScrollPane.java
@@ -0,0 +1,89 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import javax.swing.JScrollPane;
+import java.awt.Component;
+import javax.swing.ScrollPaneLayout;
+
+
+/**
+ * JLayableScrollPane.java
+ *
+ * You cant reset the layout manager on a scroll pane, due to what
+ * appears to be a bug in the JScrollPane layout, at least not it you
+ * want anything to appear on screen. You cant reset the
+ * layout manager on this class either. But you can specify what it is
+ * in the constructor.
+ *
+ * Created: Fri Mar 31 15:24:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: JLayableScrollPane.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class JLayableScrollPane extends JScrollPane
+{
+
+ public JLayableScrollPane( Component view, int vsbPolicy, int hsbPolicy )
+ {
+ this( new ScrollPaneLayout.UIResource(), view, vsbPolicy, hsbPolicy );
+ }
+
+ public JLayableScrollPane( ScrollPaneLayout layout, Component view, int vsbPolicy, int hsbPolicy )
+ {
+ // this code is culled whole scale from the super class
+ // constructor.
+ setLayout( layout );
+ setVerticalScrollBarPolicy(vsbPolicy);
+ setHorizontalScrollBarPolicy(hsbPolicy);
+ setViewport(createViewport());
+ setVerticalScrollBar(createVerticalScrollBar());
+ setHorizontalScrollBar(createHorizontalScrollBar());
+ if ( view != null) {
+ setViewportView(view);
+ }
+ updateUI();
+ }
+} // JLayableScrollPane
+
+
+
+/*
+ * ChangeLog
+ * $Log: JLayableScrollPane.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/03/31 16:21:01 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..52a315f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/MultiplexerFastAlignmentViewerCellRenderer.java
@@ -0,0 +1,180 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * MultiplexerFastAlignmentViewerCellRenderer.java
+ *
+ * This multiplexer uses three other cell renderers to render the cell.
+ * The reason for this is that as the size of the cell changes, it is
+ * necessary to alter what is drawn.
+ * <p>
+ * As a result, this renderer listens to the
+ * <code>JAlignmentViewer</code> for alterations to the size of the
+ * cell.
+ * <p>
+ * The big disadvantage to this renderer may prove its downfall - it
+ * has to make three function calls to draw the cell at normal size.
+ *
+ * Created: Fri Sep 15 19:21:54 2000
+ *
+ * @author Julian Selley
+ * @version $Id: MultiplexerFastAlignmentViewerCellRenderer.java,v 1.6 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class MultiplexerFastAlignmentViewerCellRenderer
+ implements FastAlignmentViewerCellRenderer, PropertyChangeListener
+{
+ private JAlignmentViewer viewer;
+
+ // the cell renderers to be used to render the cell
+ private ColorFastAlignmentViewerCellRenderer color;
+ private BorderFastAlignmentViewerCellRenderer border;
+ private TextFastAlignmentViewerCellRenderer text;
+ private FastAlignmentViewerCellRenderer[] viableRenderers;
+
+ private int cellWidth, cellHeight;
+
+ /* (PENDING: JNS) 15.9.00 Currently, this is only dealing with one
+ * size (i.e., not height *and* width). It may be that at a later
+ * stage we will need to split these, but for the moment I see no
+ * reason.
+ */
+ protected void calculateViableRenderers(int cellSize)
+ {
+ /* NB: hard coded values for the cut offs. It isnt necessary to be
+ * able to change these values currently on the fly.
+ *
+ * Consequently, if the cell size is smaller than 4, then only the
+ * color renderer is used. If the cell size is between 4 and 8,
+ * then the color and border renderers are used. Any greater
+ * values and all three renderers are used.
+ *
+ * If it becomes necessary for a different rendering model then
+ * this can be rewritten.
+ */
+ if (cellSize < 6) {
+ viableRenderers = new FastAlignmentViewerCellRenderer[1];
+ viableRenderers[0] = color;
+ } else if (cellSize < 16) {
+ viableRenderers = new FastAlignmentViewerCellRenderer[2];
+ viableRenderers[0] = color;
+ viableRenderers[1] = border;
+ } else {
+ viableRenderers = new FastAlignmentViewerCellRenderer[3];
+ viableRenderers[0] = color;
+ viableRenderers[1] = border;
+ viableRenderers[2] = text;
+ }
+ }
+
+ public MultiplexerFastAlignmentViewerCellRenderer(JAlignmentViewer viewer)
+ {
+ this.viewer = viewer;
+ // become a listener of the viewer
+ viewer.addPropertyChangeListener(this);
+
+ // store the width and height of the cell for small optimizations
+ this.cellWidth = viewer.getCellWidth();
+ this.cellHeight = viewer.getCellHeight();
+
+ // generate instances of the different viewers
+ color = new ColorFastAlignmentViewerCellRenderer();
+ border = new BorderFastAlignmentViewerCellRenderer();
+ text = new TextFastAlignmentViewerCellRenderer();
+
+ // calculate the dimension to use, based on which is smallest
+ if (cellWidth < cellHeight)
+ calculateViableRenderers(cellWidth);
+ else
+ calculateViableRenderers(cellHeight);
+ }
+
+ public void renderAlignmentViewerCell
+ (Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color color,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint)
+ {
+ // we need this check because this object is listening to the
+ // JAlignmentViewer.
+ if( viewer != viewer ) throw new IllegalArgumentException
+ ( "MultiplexerFastAlignmentViewer should only be used for a single JAlignmentViewer" );
+
+ // pass the call to the relevant renderers
+ for (int i = 0; i < viableRenderers.length; i++)
+ viableRenderers[i].renderAlignmentViewerCell
+ (g, x, y, width, height, viewer, element, location, color,
+ isSelected, hasFocus, isAtPoint);
+ }
+
+ public void propertyChange(PropertyChangeEvent pce)
+ {
+ if (pce.getPropertyName().equals("cellHeight") || pce.getPropertyName().equals("cellWidth" ) ){
+ cellHeight = viewer.getCellHeight();
+ cellWidth = viewer.getCellWidth();
+
+ calculateViableRenderers( Math.min( cellWidth, cellHeight ) );
+ }
+ }
+} // MultiplexerFastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: MultiplexerFastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.6 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/03/12 16:34:12 lord
+ * Alignment selection renderer added
+ *
+ * Revision 1.4 2001/01/04 14:59:42 lord
+ * Displays selected alignments correctly
+ *
+ * Revision 1.3 2000/12/13 16:32:35 lord
+ * Minor implementation improvements
+ *
+ * Revision 1.2 2000/09/21 18:39:35 jns
+ * o altering the cell size at which the border renderer kicks in and out at, to
+ * 6 from 10.
+ *
+ * Revision 1.1 2000/09/18 17:54:54 jns
+ * o created a new multiplexer cell renderer to take account of cell size
+ * o initial code
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.java b/src/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.java
new file mode 100644
index 0000000..e57519f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/NullAlignmentSelectionModel.java
@@ -0,0 +1,137 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+
+
+/**
+ * NullAlignmentSelectionModel.java
+ *
+ * Trivial selection model. Returns 0 or false for everything,
+ * and ignores selection events.
+ *
+ *
+ * Created: Mon Jan 15 13:09:41 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: NullAlignmentSelectionModel.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class NullAlignmentSelectionModel implements AlignmentSelectionModel
+{
+ private NullAlignmentSelectionModel()
+ {
+ }
+
+ public static NullAlignmentSelectionModel getInstance()
+ {
+ return inst;
+ }
+
+ private static NullAlignmentSelectionModel inst = new NullAlignmentSelectionModel();
+
+
+ public boolean isSelecting()
+ {
+ return false;
+ }
+
+
+ public SequenceAlignmentRectangle getCurrentSelection()
+ {
+ return null;
+ }
+
+
+ public int getNumberSelections()
+ {
+ return 0;
+ }
+
+ public SequenceAlignmentRectangle getSelectionAt( int index )
+ throws ArrayIndexOutOfBoundsException
+ {
+ throw new ArrayIndexOutOfBoundsException
+ ( "NullAlignmentSelectionModel does not have any selections" );
+ }
+
+ public boolean isPointSelected( SequenceAlignmentPoint point )
+ {
+ return false;
+ }
+
+ public void clearSelection()
+ {
+ }
+
+ public void clearSelection( SequenceAlignmentRectangle rectangle )
+ {
+ }
+
+ public SequenceAlignmentRectangle getRectangleAtPoint( SequenceAlignmentPoint point )
+ {
+ return null;
+ }
+
+ public SequenceAlignmentRectangle[] getRectanglesAtPoint( SequenceAlignmentPoint point )
+ {
+ return null;
+ }
+
+ public void extendSelection( SequenceAlignmentPoint point )
+ {
+ }
+
+ public void stopSelection( SequenceAlignmentPoint point )
+ {
+ }
+
+ public void addAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ }
+
+ public void removeAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ }
+} // NullAlignmentSelectionModel
+
+
+
+/*
+ * ChangeLog
+ * $Log: NullAlignmentSelectionModel.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/15 18:52:51 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.java b/src/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.java
new file mode 100644
index 0000000..4bc6dc2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/PrintableAlignmentPanel.java
@@ -0,0 +1,65 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.print.Printable;
+import javax.swing.JPanel;
+
+
+/**
+ * PrintableAlignmentPanel.java
+ *
+ *
+ * Created: Fri Mar 9 20:00:24 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: PrintableAlignmentPanel.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class PrintableAlignmentPanel extends JPanel //implements Printable
+{
+
+
+
+} // PrintableAlignmentPanel
+
+
+
+/*
+ * ChangeLog
+ * $Log: PrintableAlignmentPanel.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/03/24 19:32:05 lord
+ * Added some imports
+ *
+ * Revision 1.1 2001/03/12 16:37:07 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.java b/src/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.java
new file mode 100644
index 0000000..4444a67
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/PrintableJAlignmentViewer.java
@@ -0,0 +1,130 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import java.awt.print.PrinterException;
+import java.awt.Graphics;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import java.awt.Graphics2D;
+import java.awt.Color;
+import java.awt.Font;
+
+
+/**
+ * PrintableJAlignmentViewer.java
+ *
+ * A JAlignmentViewer which can be used to print
+ *
+ * Created: Fri Mar 9 17:21:44 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: PrintableJAlignmentViewer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class PrintableJAlignmentViewer extends JAlignmentViewer
+ implements Printable
+{
+
+ public PrintableJAlignmentViewer( SequenceAlignment msa )
+ {
+ super( msa );
+ }
+
+ // (PENDING:- PL) Want to implement these methods!
+ public void setJAlignmentViewer()
+ {
+ }
+
+ /**
+ * Set the number of cells which should be drawn across each page. This
+ * method is probably a lot more useful than cell width which is a
+ * bit blank.
+ *
+ * @param cells the number of cells per page
+ */
+ public void setXCellsPerPage( int cells )
+ {
+ }
+
+ /**
+ * Set the number of cells which should be drawn down each page. If
+ * the total size of the alignment is too big to fit, then multiple
+ * pages will have to be used. <p>
+ *
+ * If the method <code>getCellsSquare</code> returns true then this
+ * property will be ignored in preference to XCellsPerPage.
+
+ *
+ * @param cells an <code>int</code> value
+ */
+ public void setYCellsPerPage( int cells )
+ {
+ }
+
+ public void setCellsSquare( boolean square )
+ {
+ }
+
+ public boolean getCellsSquare()
+ {
+ return false;
+ }
+
+ public int print( Graphics g, PageFormat pf, int pi )
+ throws PrinterException
+ {
+ if( pi >= 1 ){
+ return Printable.NO_SUCH_PAGE;
+ }
+
+ Graphics2D g2 = (Graphics2D)g;
+ double height = pf.getImageableHeight();
+ double width = pf.getImageableWidth ();
+
+ g2.translate( pf.getImageableX(),
+ pf.getImageableY() );
+
+ paint( g2 );
+ return Printable.PAGE_EXISTS;
+ }
+} // PrintableJAlignmentViewer
+
+
+
+/*
+ * ChangeLog
+ * $Log: PrintableJAlignmentViewer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/03/12 16:37:07 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/ReadonlyException.java b/src/uk/ac/man/bioinf/gui/viewer/ReadonlyException.java
new file mode 100644
index 0000000..90a1c9a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/ReadonlyException.java
@@ -0,0 +1,96 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+
+
+
+/**
+ * ReadonlyException.java
+ *
+ *
+ * Created: Thu Dec 14 15:40:59 2000
+ *
+ * @author Julian Selley
+ * @version $Id: ReadonlyException.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ReadonlyException extends RuntimeException
+{
+ private JAlignmentViewer viewer = null; // the alignment viewer causing the exception
+
+ public ReadonlyException()
+ {
+ super("This component is read-only.");
+ }
+
+ public ReadonlyException(String message)
+ {
+ super(message);
+ }
+
+ public ReadonlyException(JAlignmentViewer jav)
+ {
+ super("This alignment viewer is in a read-only state.");
+ this.viewer = jav;
+ }
+
+ public ReadonlyException(String message, JAlignmentViewer jav)
+ {
+ super(message);
+ this.viewer = jav;
+ }
+
+ /**
+ * Returns the <code>JAlignmentViewer</code> that caused the
+ * exception, or null if the exception came from elsewhere.
+ * @see JAlignmentViewer
+ *
+ * @return the alignment viewer
+ */
+ public JAlignmentViewer getViewer()
+ {
+ return this.viewer;
+ }
+} // ReadonlyException
+
+
+
+/*
+ * ChangeLog
+ * $Log: ReadonlyException.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/04 14:26:13 jns
+ * o Bug fixing: had moved ReadonlyException to a new location, but
+ * forgot to deal with the package statements, etc.
+ *
+ * Revision 1.1 2000/12/20 16:45:01 jns
+ * o initial code
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/SequenceCursor.java b/src/uk/ac/man/bioinf/gui/viewer/SequenceCursor.java
new file mode 100644
index 0000000..9556723
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/SequenceCursor.java
@@ -0,0 +1,97 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import javax.swing.event.ChangeListener;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * SequenceCursor.java
+ *
+ *
+ * Created: Mon Apr 3 18:59:26 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceCursor.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface SequenceCursor
+{
+ /**
+ * Add a listener to this cursor
+ * @param listener the listener to add
+ */
+ public void addChangeListener( ChangeListener listener );
+
+ /**
+ * Remove the listener from this cursor
+ * @param listener the listener to remove
+ */
+ public void removeChangeListener( ChangeListener listener );
+
+ /**
+ * Set the point to the new position
+ * @param position the position to set
+ */
+ public void setPoint( SequenceAlignmentPoint position );
+
+ /**
+ * Set the mark to the current position of point
+ */
+ public void setMark();
+
+ /**
+ * Returns the position of point
+ * @return the position
+ */
+ public SequenceAlignmentPoint getPoint();
+
+ /**
+ * Returns the position of mark
+ * @return the position
+ */
+ public SequenceAlignmentPoint getMark();
+
+} // SequenceCursor
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceCursor.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.java b/src/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.java
new file mode 100644
index 0000000..aeecf46
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/SingleAlignmentSelectionModel.java
@@ -0,0 +1,191 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListenerSupport;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionEvent;
+import uk.ac.man.bioinf.gui.viewer.event.AlignmentSelectionListener;
+
+
+
+/**
+ * SingleAlignmentSelectionModel.java
+ *
+ *
+ * Created: Mon Apr 10 11:59:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SingleAlignmentSelectionModel.java,v 1.5 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class SingleAlignmentSelectionModel implements AlignmentSelectionModel
+{
+ private boolean isSelecting = false;
+ // cached rectangle
+ private SequenceAlignmentRectangle currentSelection = new SequenceAlignmentRectangle();
+ private AlignmentSelectionListenerSupport list = new AlignmentSelectionListenerSupport();
+ // points, start and stop
+ private SequenceAlignmentPoint start, stop;
+
+ public boolean isSelecting()
+ {
+ return isSelecting;
+ }
+
+ public SequenceAlignmentRectangle getCurrentSelection()
+ {
+ if( start == null ) return null;
+ return currentSelection;
+ }
+
+ public int getNumberSelections()
+ {
+ return (start == null)? 0: 1;
+ }
+
+ public SequenceAlignmentRectangle getSelectionAt( int index )
+ throws ArrayIndexOutOfBoundsException
+ {
+ if( start == null || index > 0 )
+ throw new ArrayIndexOutOfBoundsException( "No such selection rectangle" );
+
+ return getCurrentSelection();
+ }
+
+ public boolean isPointSelected( SequenceAlignmentPoint point )
+ {
+ SequenceAlignmentRectangle select = getCurrentSelection();
+
+ return ( select != null ) ? select.contains( point ): false;
+ }
+
+ public void clearSelection()
+ {
+ SequenceAlignmentRectangle rect = getCurrentSelection();
+
+ start = stop = null;
+ list.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent( this, rect, false ) );
+ isSelecting = false;
+ }
+
+ public SequenceAlignmentRectangle getRectangleAtPoint( SequenceAlignmentPoint point )
+ {
+ SequenceAlignmentRectangle select = getCurrentSelection();
+ if( select.contains( point ) ){
+ return select;
+ }
+ return null;
+ }
+
+ public SequenceAlignmentRectangle[] getRectanglesAtPoint( SequenceAlignmentPoint point )
+ {
+ SequenceAlignmentRectangle retn = getRectangleAtPoint( point );
+ if( retn == null ) return null;
+ SequenceAlignmentRectangle[] retnArray ={ retn };
+ return retnArray;
+ }
+
+ private void recalcSelectionRectangle()
+ {
+ currentSelection.setLocation( start );
+ currentSelection.setSize( 1, 1 );
+ currentSelection.add( stop );
+ }
+
+ public void extendSelection( SequenceAlignmentPoint point )
+ {
+ if( start == null || !isSelecting ){
+ start = point;
+ isSelecting = true;
+ }
+ stop = point;
+
+ recalcSelectionRectangle();
+ list.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent( this, getCurrentSelection(), isSelecting ) );
+ }
+
+ public void stopSelection( SequenceAlignmentPoint point )
+ {
+ if( start == null || !isSelecting ){
+ start = point;
+ }
+ stop = point;
+ recalcSelectionRectangle();
+ isSelecting = false;
+ list.fireAlignmentSelectionEvent
+ ( new AlignmentSelectionEvent( this, getCurrentSelection(), isSelecting ) );
+ }
+
+ public void addAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ list.addAlignmentSelectionListener( listener );
+ }
+
+ public void removeAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ list.addAlignmentSelectionListener( listener );
+ }
+} // SingleAlignmentSelectionModel
+
+
+
+/*
+ * ChangeLog
+ * $Log: SingleAlignmentSelectionModel.java,v $
+ * Revision 1.5 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2001/01/19 19:53:00 lord
+ * Removed references to variable called changed which was doing nothing
+ * at all.
+ *
+ * Revision 1.3 2001/01/15 18:55:40 lord
+ * Improved event handling.
+ * Removed one method due to interface change.
+ *
+ * Revision 1.2 2000/12/18 12:13:27 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.1 2000/04/18 17:43:56 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.2 2000/04/13 15:38:06 lord
+ * Too many changes to document. Essentially a complete re-implementation
+ *
+ * Revision 1.1 2000/04/11 16:56:23 lord
+ * Initial version. It compiles, but that does not mean it works
+ *
+ */
+
+
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.java b/src/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.java
new file mode 100644
index 0000000..6cfa318
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/TextFastAlignmentViewerCellRenderer.java
@@ -0,0 +1,103 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer; // Package name inserted by JPack
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+
+
+/**
+ * TextFastAlignmentViewerCellRenderer.java
+ *
+ * One of three classes designed to render cells in the
+ * JAlignmentViewer. This one deals specifically with drawing the
+ * character of the element in the cell.
+ * <p>
+ * By default, this will probably be drawn last, although this is
+ * determined by the RendererManager.
+ *
+ * Created: Fri Aug 25 15:11:04 2000
+ *
+ * @author Julian Selley
+ * @version $Id: TextFastAlignmentViewerCellRenderer.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class TextFastAlignmentViewerCellRenderer
+ implements FastAlignmentViewerCellRenderer
+{
+ private FontMetrics mets;
+ private char[] charArray = new char[1];
+ private int xOff, yOff, charWidth;
+
+ public TextFastAlignmentViewerCellRenderer() {}
+
+ public void renderAlignmentViewerCell
+ (Graphics g, int x, int y, int width, int height,
+ JAlignmentViewer viewer, Element element,
+ SequenceAlignmentPoint location, Color color,
+ boolean isSelected, boolean hasFocus, boolean isAtPoint)
+ {
+ // check the font metrics are the same as previously encountered
+ if (g.getFontMetrics() != mets) {
+ mets = g.getFontMetrics();
+ }
+
+ if (element != null) {
+ // draw black text
+ g.setColor(Color.black);
+
+ // set the character width
+ charWidth = mets.charWidth(element.toChar());
+
+ // calculate the offsets
+ xOff = (width - charWidth) / 2;
+ yOff = ((height + mets.getHeight()) / 2) - ((mets.getAscent() - mets.getDescent()) / 2);
+
+ // draw the character
+ charArray[0] = element.toChar();
+ g.drawChars(charArray, 0, 1, x + xOff, y + yOff);
+ }
+ }
+} // TextFastAlignmentViewerCellRenderer
+
+
+
+/*
+ * ChangeLog
+ * $Log: TextFastAlignmentViewerCellRenderer.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/18 17:54:54 jns
+ * o created a new multiplexer cell renderer to take account of cell size
+ * o initial code
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.java b/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.java
new file mode 100644
index 0000000..7637495
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionEvent.java
@@ -0,0 +1,90 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.event; // Package name inserted by JPack
+import java.util.EventObject;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+
+
+/**
+ * AlignmentSelectionEvent.java
+ *
+ *
+ * Created: Mon Apr 10 12:22:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentSelectionEvent.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class AlignmentSelectionEvent extends EventObject
+{
+ private SequenceAlignmentRectangle rectangle;
+ private boolean isAdjusting;
+
+ public AlignmentSelectionEvent( Object source, SequenceAlignmentRectangle rectangle,
+ boolean isAdjusting )
+ {
+ super( source );
+ this.rectangle = rectangle;
+ this.isAdjusting = isAdjusting;
+ }
+
+ public SequenceAlignmentRectangle getSelectionRectangle()
+ {
+ return rectangle;
+ }
+
+ public boolean isValueAdjusting()
+ {
+ return isAdjusting;
+ }
+
+ public String toString()
+ {
+ return getClass().getName() + "[" +
+ " source=" + getSource() +
+ " rectangle=" + rectangle +
+ " isAdjusting=" + isAdjusting + " ]";
+ }
+} // AlignmentSelectionEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentSelectionEvent.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/11 16:56:23 lord
+ * Initial version. It compiles, but that does not mean it works
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.java b/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.java
new file mode 100644
index 0000000..5b21c60
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListener.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.event; // Package name inserted by JPack
+import java.util.EventListener;
+
+
+/**
+ * AlignmentSelectionListener.java
+ *
+ *
+ * Created: Mon Apr 10 12:12:33 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentSelectionListener.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public interface AlignmentSelectionListener extends EventListener
+{
+ public void valueChanged( AlignmentSelectionEvent event );
+
+} // AlignmentSelectionListener
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentSelectionListener.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/11 16:56:23 lord
+ * Initial version. It compiles, but that does not mean it works
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.java b/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.java
new file mode 100644
index 0000000..6e2a6fa
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/event/AlignmentSelectionListenerSupport.java
@@ -0,0 +1,83 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.event; // Package name inserted by JPack
+import java.util.ArrayList;
+import java.util.Iterator;
+
+
+/**
+ * AlignmentSelectionListenerSupport.java
+ *
+ *
+ * Created: Mon Apr 10 12:31:19 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentSelectionListenerSupport.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class AlignmentSelectionListenerSupport
+{
+ private ArrayList listenerList = new ArrayList();
+
+ public void addAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ if( !listenerList.contains( listener ) )
+ listenerList.add( listener );
+ }
+
+ public void removeAlignmentSelectionListener( AlignmentSelectionListener listener )
+ {
+ listenerList.remove( listener );
+ }
+
+ public void fireAlignmentSelectionEvent( AlignmentSelectionEvent event )
+ {
+ Iterator iter = listenerList.iterator();
+
+ while( iter.hasNext() ){
+ ((AlignmentSelectionListener)iter.next()).valueChanged( event );
+ }
+ }
+} // AlignmentSelectionListenerSupport
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentSelectionListenerSupport.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/11 16:56:23 lord
+ * Initial version. It compiles, but that does not mean it works
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.java b/src/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.java
new file mode 100644
index 0000000..4e14024
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/event/ChangeListenerSupport.java
@@ -0,0 +1,86 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.event; // Package name inserted by JPack
+import java.util.ArrayList;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.ChangeEvent;
+import java.util.Iterator;
+
+
+/**
+ * ChangeListenerSupport.java
+ *
+ *
+ * Created: Tue Apr 4 13:31:52 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ChangeListenerSupport.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class ChangeListenerSupport
+{
+
+ private ArrayList listenerList = new ArrayList();
+
+ public void addChangeListener( ChangeListener listener )
+ {
+ if( !listenerList.contains( listener ) )
+ listenerList.add( listener );
+ }
+
+ public void removeChangeListener( ChangeListener listener )
+ {
+ listenerList.remove( listener );
+ }
+
+ public void fireChangeEvent( ChangeEvent event )
+ {
+ Iterator iter = listenerList.iterator();
+
+ while( iter.hasNext() ){
+ ((ChangeListener)iter.next()).stateChanged( event );
+ }
+ }
+} // ChangeListenerSupport
+
+
+
+/*
+ * ChangeLog
+ * $Log: ChangeListenerSupport.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.java b/src/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.java
new file mode 100644
index 0000000..45dd2fd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentRulerUI.java
@@ -0,0 +1,62 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.plaf; // Package name inserted by JPack
+import javax.swing.plaf.ComponentUI;
+
+
+/**
+ * AlignmentRulerUI.java
+ *
+ *
+ * Created: Thu Mar 23 17:10:05 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentRulerUI.java,v 1.2 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class AlignmentRulerUI extends ComponentUI
+{
+
+} // AlignmentRulerUI
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentRulerUI.java,v $
+ * Revision 1.2 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/03/27 19:00:25 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.java b/src/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.java
new file mode 100644
index 0000000..c7b6191
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/plaf/AlignmentViewerUI.java
@@ -0,0 +1,90 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.plaf; // Package name inserted by JPack
+import javax.swing.plaf.ComponentUI;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import java.awt.Point;
+import java.awt.Rectangle;
+
+
+/**
+ * AlignmentViewerUI.java
+ *
+ *
+ * Created: Tue Mar 14 16:29:34 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentViewerUI.java,v 1.4 2001/04/11 17:04:42 lord Exp $
+ */
+
+public abstract class AlignmentViewerUI extends ComponentUI
+{
+ public abstract SequenceAlignmentPoint getSequencePointAtPoint( int x, int y );
+
+ public SequenceAlignmentPoint getSequencePointAtPoint( Point point )
+ {
+ return getSequencePointAtPoint( point.x, point.y );
+ }
+
+ public abstract Point getPointAtSequencePoint( int x, int y );
+
+ public Point getPointAtSequencePoint( SequenceAlignmentPoint point )
+ {
+ return getPointAtSequencePoint( point.getX(), point.getY() );
+ }
+
+ public abstract Rectangle getCellBounds( SequenceAlignmentPoint point );
+} // AlignmentViewerUI
+
+/*
+ * ChangeLog
+ * $Log: AlignmentViewerUI.java,v $
+ * Revision 1.4 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/02 14:50:58 jns
+ * o changed to extend the ComponentUI rather than the SliderUI - makes
+ * more sense
+ *
+ * Revision 1.2 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.3 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.2 2000/03/27 18:50:30 lord
+ * Now extends BasicSliderUI, as this had done most of the work
+ *
+ * Revision 1.1 2000/03/16 16:19:20 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.java b/src/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.java
new file mode 100644
index 0000000..6b563b4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentRulerUI.java
@@ -0,0 +1,181 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.plaf; // Package name inserted by JPack
+import javax.swing.plaf.basic.BasicSliderUI;
+import javax.swing.JSlider;
+import java.awt.Graphics;
+import javax.swing.plaf.ComponentUI;
+import javax.swing.JComponent;
+import java.awt.Dimension;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentRuler;
+
+
+/**
+ * BasicAlignmentRulerUI.java
+ *
+ *
+ * Created: Thu Mar 23 17:10:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: BasicAlignmentRulerUI.java,v 1.3 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class BasicAlignmentRulerUI extends BasicSliderUI
+{
+
+ private JAlignmentRuler ruler;
+
+ public BasicAlignmentRulerUI( JComponent comp )
+ {
+ super( (JSlider)comp );
+ this.ruler = (JAlignmentRuler)comp;
+ }
+
+
+ private Dimension prefSize = new Dimension();
+ public Dimension getPreferredSize( JComponent comp )
+ {
+ prefSize.setSize
+ ( ruler.getPreferredWidthPerBase() * ruler.getSequenceAlignment().getLength(),
+ ruler.getPreferredHeight() );
+ return prefSize;
+ }
+
+
+ protected void recalculateIfInsetsChanged()
+ {
+ // This method is overriden because we automatically recalculate
+ // every time anyway so there is no point doing it twice.
+ }
+
+ public void paint( Graphics g, JComponent c )
+ {
+ // force this every time. If we do not there are a lot of problems
+ // with using this component as a renderer.
+ calculateGeometry();
+ super.paint( g, c );
+ }
+
+
+ public void paintThumb( Graphics g )
+ {
+ // get rid of this as we dont want it for the ruler
+ }
+
+ public void paintTrack( Graphics g )
+ {
+ // get rid of this as we dont want if for the ruler
+ }
+
+
+ int oldWidth, oldHeight = 0;
+ protected void calculateGeometry()
+ {
+ // the CellRendererPane resizes the comp to 0, 0 after it renders.
+ // The comp then recalcs its geometries all wrong, for the next
+ // rendering, and all the contents dissappear. This prevents all
+ // that.
+ int height = slider.getHeight();
+ int width = slider.getWidth();
+ if( width == 0 || height == 0 )
+ return;
+
+ // only do the calculation when we actually need to.
+ if( height == oldHeight && width == oldWidth )
+ return;
+
+ oldHeight = height;
+ oldWidth = width;
+
+ super.calculateGeometry();
+ }
+
+ // this is irrelevant so why calculate it?
+ protected void calculateTrackBuffer()
+ {
+ }
+
+ protected void calculateTrackRect()
+ {
+ // mostly straight from super class
+ trackRect.x = contentRect.x;
+ trackRect.y = contentRect.y;
+ trackRect.width = contentRect.width - (trackBuffer * 2);
+ // Ive set this to four or the ticks start right at the top which
+ // is a little bit ugly..
+ trackRect.height = 4;
+ }
+
+ protected void calculateThumbLocation()
+ {
+ thumbRect.x = thumbRect.y = thumbRect.height = thumbRect.width = 0;
+ }
+
+
+ public static ComponentUI createUI( JComponent comp )
+ {
+ return new BasicAlignmentRulerUI( comp );
+ }
+
+} // BasicAlignmentRulerUI
+
+
+
+/*
+ * ChangeLog
+ * $Log: BasicAlignmentRulerUI.java,v $
+ * Revision 1.3 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.4 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.3 2000/03/31 16:25:24 lord
+ * Changed the way in which geometry is calculated to ensure that this
+ * class be used as a cell renderer. Subsequently Ive stopped using this
+ * class as a cell renderer so possible this is now obsolete, but I think
+ * it makes sense to leave this stuff in regardless in case I choose to
+ * do this again.
+ *
+ * Revision 1.2 2000/03/29 14:58:03 lord
+ * Added preferred size calculations, and changed the calculation of the
+ * track rectangle so that it doesnt take up room I dont want it too.
+ *
+ * Revision 1.1 2000/03/27 19:00:36 lord
+ * Initial checkin
+ *
+ */
+
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.java b/src/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.java
new file mode 100644
index 0000000..3590907
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/plaf/BasicAlignmentViewerUI.java
@@ -0,0 +1,1061 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+
+ */
+
+package uk.ac.man.bioinf.gui.viewer.plaf; // Package name inserted by JPack
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.InputEvent;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import javax.swing.CellRendererPane;
+import javax.swing.JComponent;
+import javax.swing.KeyStroke;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.MouseInputListener;
+import javax.swing.plaf.ComponentUI;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.gui.viewer.AlignmentSelectionModel;
+import uk.ac.man.bioinf.gui.viewer.AlignmentViewerCellRenderer;
+import uk.ac.man.bioinf.gui.viewer.FastAlignmentViewerCellRenderer;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentPoint;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.gui.viewer.AlignmentSelectionRenderer;
+import uk.ac.man.bioinf.gui.viewer.DefaultAlignmentSelectionRenderer;
+
+
+/**
+ * BasicAlignmentViewerUI.java
+ *
+ *
+ * Created: Tue Mar 14 16:30:36 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: BasicAlignmentViewerUI.java,v 1.28 2001/04/11 17:04:42 lord Exp $
+ */
+
+public class BasicAlignmentViewerUI extends AlignmentViewerUI
+ implements PropertyChangeListener, MouseInputListener
+{
+ // the main panel on which to render things, defeating upwards
+ // propogation of the paint, and validate calls
+ private CellRendererPane rendererPane;
+ // all of these come from the JAlignmentViewer, which we store here
+ // to save time.
+ private JAlignmentViewer viewer;
+ private int cellWidth, cellHeight;
+ private AlignmentViewerCellRenderer renderer;
+ private FastAlignmentViewerCellRenderer fastRenderer;
+ private AlignmentSelectionRenderer selectionRenderer;
+ private SequenceAlignment alignment;
+ private SequenceAlignmentPoint cursorLocation = new SequenceAlignmentPoint();
+ private AlignmentSelectionModel selectionModel;
+ private boolean selectingToggle = false;
+
+ public BasicAlignmentViewerUI()
+ {
+ }
+
+ public static ComponentUI createUI( JComponent comp )
+ {
+ return new BasicAlignmentViewerUI();
+ }
+
+
+ public void installUI( JComponent comp )
+ {
+ // make a new CellRendererPane. This class defeats upwards
+ // propogation of paint, and validate requests which we dont
+ // want.
+ //using new renderer pane
+ rendererPane = new CellRendererPane();
+ comp.add( rendererPane );
+ // store the main component.
+ viewer = (JAlignmentViewer)comp;
+ // store the cell height and width. We will definately use,
+ // repeatedly, so we might as well save them to save method invocations
+ cellWidth = viewer.getCellWidth();
+ cellHeight = viewer.getCellHeight();
+ // like wise the cell renderer and alignment
+ renderer = viewer.getCellRenderer();
+ fastRenderer = viewer.getFastCellRenderer();
+ selectionRenderer = viewer.getAlignmentSelectionRenderer();
+ alignment = viewer.getSequenceAlignment();
+ //ruler = viewer.getJAlignmentRuler();
+ //rendererPane.add( ruler );
+ selectionModel = viewer.getSelectionModel();
+
+ installListeners();
+ }
+
+ public void uninstallUI( JComponent comp )
+ {
+ uninstallListeners();
+ }
+
+
+ public void installListeners()
+ {
+ viewer.addPropertyChangeListener( this );
+ installKeyboardActions( viewer );
+ viewer.addMouseListener(this);
+ viewer.addMouseMotionListener(this);
+ viewer.addPropertyChangeListener( this );
+ viewer.addFocusListener
+ ( new FocusListener(){
+ public void focusGained( FocusEvent event )
+ {
+ BasicAlignmentViewerUI.this.viewer.repaint();
+ }
+
+ public void focusLost( FocusEvent event )
+ {
+ BasicAlignmentViewerUI.this.viewer.repaint();
+ }
+ });
+ viewer.addCursorChangeListener( new PointListener() );
+ }
+
+ public void uninstallListeners()
+ {
+ viewer.removePropertyChangeListener( this );
+ viewer.removeMouseListener(this);
+ viewer.removeMouseMotionListener(this);
+ }
+
+
+ // this is instance variable just to save on the object allocation
+ private SequenceAlignmentPoint rendererLocation = new SequenceAlignmentPoint();
+
+ public Rectangle paintFocusRect( Graphics g, Rectangle rect )
+ {
+ g.setColor( Color.black );
+ g.drawRect( rect.x, rect.y, rect.width - 1, rect.height - 1 );
+ rect.x -= 1;
+ rect.y -= 1;
+ rect.height -= 2;
+ rect.width -= 2;
+ return rect;
+ }
+
+ public void paint( Graphics g, JComponent c )
+ {
+ Rectangle rect = g.getClipBounds();
+
+ if( c.hasFocus() ){
+ rect = paintFocusRect( g, rect );
+ }
+
+ paintCells( g, c );
+ paintSelection( g, c );
+ }
+
+ protected void paintCells( Graphics g, JComponent c )
+ {
+ Rectangle rect = g.getClipBounds();
+
+ // calculate where to start drawing. We need to draw 1 either side
+ // of the actuall clipping area though.
+ int topLeftIndex = getSequencePointAtPoint( rect.x, rect.y ).getY() - 1;
+ topLeftIndex = (topLeftIndex < 1) ? 1: topLeftIndex;
+ int topLeftPosition = getSequencePointAtPoint( rect.x, rect.y ).getX() - 1;
+ topLeftPosition = ( topLeftPosition < 1 ) ? 1 : topLeftPosition;
+ int topRightPosition = getSequencePointAtPoint( rect.x + rect.width, rect.y ).getX() + 1;
+ int bottomLeftIndex = getSequencePointAtPoint( rect.x, rect.y + rect.height ).getY() + 1;
+
+ // calc the start Y position.. We substract 1 because we
+ // want cell number 1 to draw at position zero
+ int currY = (cellHeight * (topLeftIndex - 1)) + c.getInsets().top;
+
+ // iterate through all of the cells.
+ for( int j = topLeftIndex; j < bottomLeftIndex; j++ ){
+
+ // we now iterate through the sequence elements in three
+ // steps. First the nulls at the
+ int startSeq = topLeftPosition;
+ int endSeq = topRightPosition;
+
+ // if we are off the bottom of the sequences then just pretend
+ // that we never get to the sequence
+
+ if( j >= alignment.getNumberSequences() + 1){
+ startSeq = topRightPosition;
+ }
+ else{
+ int temp;
+ // else work out where the sequence starts at least if we are
+ // not already into it.
+ if( topLeftPosition < (temp = alignment.getInset( j ) + 1) ){
+ startSeq = temp;
+ }
+ // and then work out where the end of the sequence is at least
+ // if we get to it.
+ if( topRightPosition > (temp = alignment.getInset( j ) + alignment.getSequenceAt( j ).getGappedLength() + 1) ){
+ endSeq = temp;
+ }
+ }
+
+ for( int i = topLeftPosition; i < startSeq -1; i ++ ){
+
+ rendererLocation.setLocation( i, j );
+
+ // is code reuse really worth this????
+ renderCell( g, (i - 1) * cellWidth, currY, cellWidth, cellHeight, rect, rendererLocation, null );
+ }
+
+ for( int i = startSeq; i < endSeq; i ++ ){
+
+ rendererLocation.setLocation( i, j );
+ Element element = alignment.getSequenceAt( j ).getGappedElementAt
+ ( i - alignment.getInset( j ) );
+
+ // is code reuse really worth this????
+ renderCell( g, (i - 1) * cellWidth, currY, cellWidth, cellHeight, rect, rendererLocation, element );
+ }
+
+ for( int i = endSeq + 1; i < topRightPosition; i++ ){
+
+ rendererLocation.setLocation( i, j );
+
+ // is code reuse really worth this????
+ renderCell( g, (i - 1) * cellWidth, currY, cellWidth, cellHeight, rect, rendererLocation, null );
+ }
+
+ currY += cellHeight;
+ }
+ }
+
+ protected void paintSelection( Graphics g, JComponent c )
+ {
+ Rectangle rect = g.getClipBounds();
+ //g.setClip( rect.x, rect.y, rect.width, rect.height );
+ //g.clipRect( rect.x, rect.y, rect.width, rect.height );
+
+ SequenceAlignmentRectangle clipSeqRect = getSequenceAlignmentRectangleAtRectangle( rect );
+
+ for( int i = 0; i < selectionModel.getNumberSelections(); i++ ){
+ SequenceAlignmentRectangle selRect = selectionModel.getSelectionAt( i );
+ if( true ){ //selRect.intersects( clipSeqRect ) ){
+ Point leftTop = getPointAtSequencePoint( selRect.getX(), selRect.getY() );
+ Point bottomRight = getPointAtSequencePoint( (selRect.getWidth() + selRect.getX()),
+ (selRect.getHeight() + selRect.getY() ) );
+
+ // g.setClip( rect.x, rect.y, rect.width, rect.height );
+ // g.setClip( leftTop.x, leftTop.y, (bottomRight.x - leftTop.x), (bottomRight.y - leftTop.y) );
+ //g.clipRect( rect.x, rect.y, rect.width, rect.height );
+ selectionRenderer.renderAlignmentSelection
+ ( g, leftTop.x, leftTop.y, (bottomRight.x - leftTop.x), (bottomRight.y - leftTop.y),
+ viewer, selRect );
+ }
+ }
+ }
+
+ protected void repaint( SequenceAlignmentPoint point )
+ {
+ viewer.repaint( getCellBounds( point ) );
+ }
+
+ protected void paintImmediately( SequenceAlignmentPoint point )
+ {
+ viewer.paintImmediately( getCellBounds( point ) );
+ }
+
+ protected void renderCell
+ ( Graphics g, int currX, int currY, int cellWidth, int cellHeight,
+ Rectangle rect, SequenceAlignmentPoint rendererLocation, Element element )
+ {
+ //if( true ) return ;
+ // not quite sure what this does, but it looks good. Hopefully
+ // though it should stop naughty renderers from doing evil
+ // things to the layout.
+ //g.setClip( currX, currY, cellWidth, cellHeight );
+ //g.clipRect( rect.x, rect.y, rect.width, rect.height );
+
+ Color bgColor = viewer.getColorMap().getColorAt(alignment, element, rendererLocation);
+ boolean isSelected = selectionModel.isPointSelected( rendererLocation );
+ boolean hasFocus = viewer.hasFocus();
+ boolean isAtPoint = rendererLocation.equals( cursorLocation );
+
+ if( renderer == null ){
+ fastRenderer.renderAlignmentViewerCell
+ ( g, currX, currY, cellWidth, cellHeight,
+ viewer, element, rendererLocation,
+ bgColor, isSelected, hasFocus, isAtPoint );
+ }
+ else{
+ Component cell = renderer.getAlignmentViewerCellRendererComponent
+ ( viewer,
+ element,
+ rendererLocation,
+ bgColor,
+ isSelected,
+ hasFocus,
+ isAtPoint );
+
+ rendererPane.paintComponent( g, cell, viewer, currX, currY,
+ cellWidth, cellHeight, true );
+
+ }
+
+ // support for an XOR cursor blink. If the we are drawing the
+ // right cell just XOR it...
+ if( getBlinkOn() && rendererLocation.equals( cursorBlinkPoint ) ){
+ // now that we have drawn do the XOR as the blink is on.
+ g.setXORMode( Color.white );
+ g.fillRect( currX, currY, cellWidth, cellHeight );
+ g.setPaintMode();
+ }
+ }
+
+ private SequenceAlignmentRectangle seqRect = new SequenceAlignmentRectangle();
+ public SequenceAlignmentRectangle getSequenceAlignmentRectangleAtRectangle( Rectangle rect )
+ {
+ seqRect.setLocation( getSequencePointAtPoint( (int)rect.getX(), (int)rect.getY() ) );
+
+ SequenceAlignmentPoint loc = getSequencePointAtPoint
+ ( (int)(rect.getX() + rect.getWidth()), (int)(rect.getY() + rect.getHeight()) );
+
+
+ seqRect.setSize( loc.getX() - seqRect.getX(), loc.getY() - seqRect.getY() );
+ return seqRect;
+ }
+
+
+ private SequenceAlignmentPoint loc = new SequenceAlignmentPoint( 0, 0 );
+ public SequenceAlignmentPoint getSequencePointAtPoint( int x, int y )
+ {
+ // need to think about this. Is there a problem here with
+ // downwards rounding???
+
+ // also this ignores the insets issue for the moment, which is
+ // something else I need to think about.
+ // ignore all the insets for the moment.
+
+ int sequencePos = (x / cellWidth) + 1;
+ int alignmentLoc = (y / cellHeight) + 1;
+
+ loc.setLocation
+ ( sequencePos, alignmentLoc );
+ return loc;
+ }
+
+ public Point getPointAtSequencePoint( int x, int y )
+ {
+ return new Point
+ ( (x - 1) * cellWidth,
+ (y - 1) * cellHeight );
+ }
+
+ public Point getPointAtSequencePoint( SequenceAlignmentPoint point )
+ {
+ return getPointAtSequencePoint
+ ( point.getX(),
+ point.getY() );
+ }
+
+ public Rectangle getCellBounds( SequenceAlignmentPoint point )
+ {
+ return getCellBounds( point, null );
+ }
+
+ public Rectangle getCellBounds( SequenceAlignmentPoint point, Rectangle rect )
+ {
+ if( rect == null ) rect = new Rectangle();
+ Point physPoint = getPointAtSequencePoint( point );
+ rect.setLocation( physPoint.x, physPoint.y );
+ rect.setSize( cellWidth, cellHeight );
+ return rect;
+ }
+
+ // (PENDING:- PL) These should be protected methods...
+ private Rectangle blinkedCursor = new Rectangle();
+ private SequenceAlignmentPoint cursorBlinkPoint;
+ private boolean blinkOn = false;
+ private CursorBlinkThread cursorThread;
+
+ // I've put these into private methods so that I could debug when
+ // the values were being changed
+ private synchronized void setBlinkOn( boolean on )
+ {
+ blinkOn = on;
+ }
+
+ private boolean getBlinkOn()
+ {
+ return blinkOn;
+ }
+
+ public synchronized void setCursorBlink()
+ {
+ if( cursorThread == null ){
+ cursorThread = new CursorBlinkThread();
+ cursorThread.start();
+ }
+
+ // cache the current
+ SequenceAlignmentPoint oldCursor
+ = cursorBlinkPoint;
+
+ //get the cursor position
+ cursorBlinkPoint =
+ viewer.getCursorModel().getPoint();
+
+ if( getBlinkOn() ){
+ // we do not want to unset the cursor again!
+ cursorThread.interrupt();
+ // need to wipe old blink. Do this by just painting over it.
+ paintImmediately( oldCursor );
+ }
+
+
+ getCellBounds( cursorBlinkPoint, blinkedCursor );
+ setBlinkOn( true );
+ // this should repaint with XOR
+ repaint( cursorBlinkPoint );
+
+
+ cursorThread.notifyImpl();
+ }
+
+ public synchronized void unsetCursorBlink()
+ {
+ setBlinkOn( false );
+ paintImmediately( cursorBlinkPoint );
+ }
+
+ class CursorBlinkThread extends Thread
+ {
+ public void run()
+ {
+ while( true ){
+ try{
+ sleep( 75 );
+ BasicAlignmentViewerUI.this.unsetCursorBlink();
+ waitImpl();
+ }
+ catch( InterruptedException iep ){
+ // we can safely ignore this.
+ }
+ catch( Throwable t ){
+ t.printStackTrace();
+ }
+ }
+ }
+
+ public synchronized void waitImpl() throws InterruptedException
+ {
+ this.wait();
+ }
+
+ public synchronized void notifyImpl()
+ {
+ this.notify();
+ }
+ }
+
+ // implementation of java.beans.PropertyChangeListener interface
+ public void propertyChange( PropertyChangeEvent pce )
+ {
+ if( pce.getPropertyName().equals( "cellHeight" ) ){
+
+ Rectangle rectangle = viewer.getVisibleRect();
+ // this is the sequence point before we have changed the cellHeight.
+ SequenceAlignmentPoint seqPoint = getSequencePointAtPoint
+ ( rectangle.getLocation() );
+
+ cellHeight = ((Integer)pce.getNewValue()).intValue();
+
+ // now get the new location of the old SequenceAlignmentPoint
+ Point newPoint = getPointAtSequencePoint( seqPoint );
+
+ // which is the point that we want to make the top left. The old
+ // size and so forth are correct.
+ rectangle.setLocation( newPoint );
+
+ viewer.scrollRectToVisible( rectangle );
+ }
+
+ else if( pce.getPropertyName().equals( "cellWidth" ) ){
+
+ Rectangle rectangle = viewer.getVisibleRect();
+ // this is the sequence point before we have changed the cellHeight.
+ SequenceAlignmentPoint seqPoint = getSequencePointAtPoint
+ ( rectangle.getLocation() );
+
+ cellWidth = ((Integer)pce.getNewValue()).intValue();
+
+ // now get the new location of the old SequenceAlignmentPoint
+ Point newPoint = getPointAtSequencePoint( seqPoint );
+
+ // which is the point that we want to make the top left. The old
+ // size and so forth are correct.
+ rectangle.setLocation( newPoint );
+
+ viewer.scrollRectToVisible( rectangle );
+ }
+
+ else if( pce.getPropertyName().equals( "fastCellRenderer" ) ){
+ fastRenderer = (FastAlignmentViewerCellRenderer)pce.getNewValue();
+ }
+
+ else if( pce.getPropertyName().equals( "cellRenderer" ) ){
+ renderer = (AlignmentViewerCellRenderer)pce.getNewValue();
+ }
+
+ else if( pce.getPropertyName().equals( "alignmentSelectionRenderer" ) ){
+ selectionRenderer = (AlignmentSelectionRenderer)pce.getNewValue();
+ }
+
+ else if( pce.getPropertyName().equals( "sequenceAlignment" ) ){
+ alignment = (SequenceAlignment)pce.getNewValue();
+ }
+
+ else if( pce.getPropertyName().equals( "alignmentSelectionModel" ) ){
+ selectionModel = (AlignmentSelectionModel)pce.getNewValue();
+ }
+
+ // if read-only change
+ else if (pce.getPropertyName().equals("readonly")) {
+ if (((Boolean)pce.getNewValue()).booleanValue())
+ // uninstall the mouse motion listener
+ viewer.removeMouseMotionListener(this);
+ else
+ // install the mouse motion listener
+ viewer.addMouseMotionListener(this);
+ }
+ }
+
+ protected void installKeyboardActions( JAlignmentViewer viewer )
+ {
+ viewer.registerKeyboardAction
+ ( new SelectionToggler(), KeyStroke.getKeyStroke
+ ( KeyEvent.VK_ENTER, 0 ), JComponent.WHEN_IN_FOCUSED_WINDOW );
+
+ viewer.registerKeyboardAction
+ ( new SelectionClearer(), KeyStroke.getKeyStroke
+ ( KeyEvent.VK_BACK_SPACE, 0 ), JComponent.WHEN_IN_FOCUSED_WINDOW );
+
+ // key ' ' to insert a gap at the cursor
+ viewer.registerKeyboardAction
+ (new ActionListener() {
+ public void actionPerformed(ActionEvent e)
+ {
+ try {
+ BasicAlignmentViewerUI.this.viewer.insertGapsAtCursor(1);
+ } catch (SequenceVetoException ex) {
+ Debug.both
+ (this, "JAlignmentViewer: Can't insert gap - it was vetoed!", ex);
+ } catch (AlignmentVetoException ex) {
+ Debug.both
+ (this, "JAlignmentViewer: Can't insert gap - it was vetoed!", ex);
+ }
+ }
+ }, KeyStroke.getKeyStroke(KeyEvent.VK_SPACE, 0),
+ JComponent.WHEN_IN_FOCUSED_WINDOW);
+
+ // key 'DEL' to remove a gap at the cursor
+ viewer.registerKeyboardAction
+ (new ActionListener() {
+ public void actionPerformed(ActionEvent e)
+ {
+ try {
+ BasicAlignmentViewerUI.this.viewer.deleteGapsAtCursor(1);
+ } catch (SequenceVetoException ex) {
+ Debug.both
+ (this, "JAlignmentViewer: Can't delete gap - it was vetoed!", ex);
+ } catch (AlignmentVetoException ex) {
+ Debug.both
+ (this, "JAlignmentViewer: Can't delete gap - it was vetoed!", ex);
+ }
+ }
+ }, KeyStroke.getKeyStroke(KeyEvent.VK_DELETE, 0),
+ JComponent.WHEN_IN_FOCUSED_WINDOW);
+
+ registerKey(KeyEvent.VK_RIGHT, KeyScroller.RIGHT );
+ registerKey(KeyEvent.VK_LEFT, KeyScroller.LEFT );
+ registerKey(KeyEvent.VK_DOWN, KeyScroller.DOWN );
+ registerKey(KeyEvent.VK_UP, KeyScroller.UP );
+
+ registerKey("KP_RIGHT", KeyScroller.RIGHT );
+ registerKey("KP_LEFT", KeyScroller.LEFT );
+ registerKey("KP_DOWN", KeyScroller.DOWN );
+ registerKey("KP_UP", KeyScroller.UP );
+ }
+
+ //(PENDING:- PL) This needs to be more generic, so that it can
+ // handle to end/to begining events and so forth. Keep it simple at first!!!
+ protected void registerKey( String keyEvent, int direction )
+ {
+ viewer.registerKeyboardAction
+ ( new KeyScroller( viewer, direction ),
+ KeyStroke.getKeyStroke( keyEvent ),
+ JComponent.WHEN_IN_FOCUSED_WINDOW );
+ }
+
+ protected void registerKey( int keyEvent, int direction )
+ {
+ viewer.registerKeyboardAction
+ ( new KeyScroller( viewer, direction ),
+ KeyStroke.getKeyStroke( keyEvent, 0 ),
+ JComponent.WHEN_IN_FOCUSED_WINDOW );
+ }
+
+ public void mouseClicked(MouseEvent e)
+ {
+ viewer.moveCursor(getSequencePointAtPoint(e.getPoint()));
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ /* Currently this method is not used. Code may be provided for
+ * functionality at a later stage.
+ */
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ /* Currently this method is not used. Code may be provided for
+ * functionality at a later stage.
+ */
+ }
+
+ private SequenceAlignmentPoint originalSequencePoint = null;
+ private SequenceAlignmentPoint currentSequencePoint = null;
+ private int originalMouseY = 0;
+
+ // this is the last place that point we signalled as an extended
+ // selection. If the new event it the same place we can ignore it.
+ private SequenceAlignmentPoint lastExtendedSelectionPoint = new SequenceAlignmentPoint();
+
+ public void mousePressed(MouseEvent e)
+ {
+ // if button 2 is down, then we want to extend the selection
+ if( ( e.getModifiers() & InputEvent.BUTTON2_MASK ) == InputEvent.BUTTON2_MASK ){
+
+ // clear the selection model it is not selecting.
+ if( !selectionModel.isSelecting() ){
+ selectionModel.clearSelection();
+ }
+
+ // signal the change
+ selectionModel.extendSelection
+ ( new SequenceAlignmentPoint
+ ( getSequencePointAtPoint( e.getX(), e.getY() ) ) );
+
+ // and remember this point.
+ lastExtendedSelectionPoint.setLocation
+ ( getSequencePointAtPoint( e.getX(), e.getY() ) );
+
+ }
+ else{
+ // set the original sequence point at mouse down
+ originalSequencePoint = new SequenceAlignmentPoint
+ (getSequencePointAtPoint(e.getX(), e.getY()));
+ // store the Y location to prevent drifting
+ originalMouseY = e.getY();
+ }
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ // if button 2 is down, then we want to stop the selection
+ if( ( e.getModifiers() & InputEvent.BUTTON2_MASK ) == InputEvent.BUTTON2_MASK ){
+ selectionModel.stopSelection
+ ( new SequenceAlignmentPoint
+ ( getSequencePointAtPoint( e.getX(), e.getY() ) ) );
+ }
+ else{
+ // move the cursor to the current location
+ if (currentSequencePoint != null)
+ viewer.moveCursor(currentSequencePoint);
+
+ // reset the variables
+ originalSequencePoint = null;
+ originalMouseY = 0;
+ currentSequencePoint = null;
+ }
+ }
+
+ public void mouseDragged(MouseEvent e)
+ {
+ // if button 2 is down, then we want to extend the selection
+ if( ( e.getModifiers() & InputEvent.BUTTON2_MASK ) == InputEvent.BUTTON2_MASK ){
+ // where have we dragged to.
+ SequenceAlignmentPoint nowAtPoint = getSequencePointAtPoint( e.getX(), e.getY() );
+
+ // if drag has moved us into a new region signal an event
+ if( !nowAtPoint.equals( lastExtendedSelectionPoint ) ){
+ selectionModel.extendSelection
+ ( new SequenceAlignmentPoint( nowAtPoint ) );
+ lastExtendedSelectionPoint.setLocation( nowAtPoint );
+ }
+ }
+ else{
+ // if we are still in the viewer
+ if ((viewer.contains(e.getPoint())) || (originalSequencePoint != null)) {
+ // get the current sequence point
+ currentSequencePoint = new SequenceAlignmentPoint
+ (getSequencePointAtPoint(e.getX(), originalMouseY));
+
+ // the difference between the two points
+ int difference = currentSequencePoint.getX() -
+ originalSequencePoint.getX();
+
+ // return if we havent gone anywhere significant
+ if (difference == 0)
+ return;
+
+ // if inserting gaps
+ if (difference > 0) {
+ try {
+ // insert the gaps
+ viewer.insertGapsAt(originalSequencePoint, difference);
+ // set the current position to the original insert point to
+ // avoid odd behavior
+ originalSequencePoint = new SequenceAlignmentPoint
+ (currentSequencePoint);
+ } catch (SequenceVetoException excep) {
+ /* (PENDING: JNS) 31.10.00 Wasnt sure what to do with this,
+ * so for the time being it is just being chucked out to the
+ * debug.
+ */
+ Debug.both(this, "Cannot insert a gap here - it was vetoed!", excep);
+ } catch (AlignmentVetoException excep) {
+ /* (PENDING: JNS) 31.10.00 Wasnt sure what to do with this,
+ * so for the time being it is just being chucked out to the
+ * debug.
+ */
+ Debug.both(this, "Cannot insert a gap here - it was vetoed!", excep);
+ }
+ // if deleting gaps
+ } else if (difference < 0) {
+ try {
+ // get the number of gaps downstream
+ int maxNumberGapsUpstream =
+ Sequences.getNumberGapsUpstreamFrom
+ (currentSequencePoint.getX() -
+ alignment.getInset(originalSequencePoint.getY()),
+ alignment.getSequenceAt(originalSequencePoint.getY()));
+
+ // if able to delete all gaps requested (this inc. the inset gaps)
+ if (((currentSequencePoint.getX() <
+ alignment.getInset(originalSequencePoint.getY()) + 1) &&
+ (-(difference) < alignment.
+ getInset(originalSequencePoint.getY()) + 1)) ||
+ (maxNumberGapsUpstream > -(difference)))
+ // delete the gaps
+ viewer.deleteGapsAt(currentSequencePoint.getX(),
+ originalSequencePoint.getY(),
+ -(difference));
+ // otherwise remove the max number of gaps possible
+ else
+ viewer.deleteGapsAt(currentSequencePoint.getX(),
+ originalSequencePoint.getY(),
+ maxNumberGapsUpstream);
+
+ /* if gaps were deleted (i.e., maxNumberGapsUpstream != 0
+ * then move the original insert point, otherwise don't
+ */
+ if (maxNumberGapsUpstream != 0)
+ // set the current position to the original insert point
+ originalSequencePoint = new SequenceAlignmentPoint
+ (currentSequencePoint);
+ } catch (NoGapAtThisPositionException excep) {
+ // this should not happen (I think)
+ Debug.both(this, "Cannot remove a gap here!", excep);
+ } catch (SequenceVetoException excep) {
+ Debug.both(this, "Cannot remove a gap here - it was vetoed!", excep);
+ } catch (AlignmentVetoException excep) {
+ Debug.both(this, "Cannot remove a gap here - it was vetoed!", excep);
+ }
+ } else return;
+ }
+ }
+ }
+
+ public void mouseMoved(MouseEvent e)
+ {
+ /* Currently this method is not used. Code may be provided for
+ * functionality at a later stage.
+ */
+ }
+
+ public class PointListener implements ChangeListener
+ {
+ public void stateChanged( ChangeEvent event )
+ {
+ BasicAlignmentViewerUI.this.cursorLocation =
+ BasicAlignmentViewerUI.this.viewer.getPoint();
+
+ if( BasicAlignmentViewerUI.this.selectingToggle ){
+ BasicAlignmentViewerUI.this.viewer.extendSelection
+ ( BasicAlignmentViewerUI.this.viewer.getPoint() );
+ }
+ BasicAlignmentViewerUI.this.setCursorBlink();
+ }
+ }
+
+ public class SelectionClearer implements ActionListener
+ {
+ public void actionPerformed( ActionEvent event )
+ {
+ BasicAlignmentViewerUI.this.viewer.clearSelection();
+ BasicAlignmentViewerUI.this.selectingToggle = false;
+ }
+ }
+
+ public class SelectionToggler implements ActionListener
+ {
+ public void actionPerformed( ActionEvent event )
+ {
+ if( BasicAlignmentViewerUI.this.selectingToggle ){
+ BasicAlignmentViewerUI.this.selectingToggle = false;
+ }
+ else{
+ BasicAlignmentViewerUI.this.selectingToggle = true;
+ BasicAlignmentViewerUI.this.viewer.extendSelection
+ ( BasicAlignmentViewerUI.this.viewer.getPoint() );
+ }
+ }
+ }
+
+ public class KeyScroller implements ActionListener
+ {
+ private JAlignmentViewer viewer;
+ private int direction;
+
+ public static final int UP = 1;
+ public static final int DOWN = 2;
+ public static final int RIGHT = 3;
+ public static final int LEFT = 4;
+
+ public KeyScroller( JAlignmentViewer viewer, int direction )
+ {
+ this.viewer = viewer;
+ this.direction = direction;
+ }
+
+ public void actionPerformed( ActionEvent event )
+ {
+ switch (direction){
+
+ case UP:
+ viewer.moveCursorUp( 1 );
+ break;
+ case DOWN:
+ viewer.moveCursorDown( 1 );
+ break;
+ case RIGHT:
+ viewer.moveCursorRight( 1 );
+ break;
+ case LEFT:
+ viewer.moveCursorLeft( 1 );
+ break;
+ }
+ }
+ }
+} // BasicAlignmentViewerUI
+
+
+
+/*
+ * ChangeLog
+ * $Log: BasicAlignmentViewerUI.java,v $
+ * Revision 1.28 2001/04/11 17:04:42 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.27 2001/03/12 17:05:00 lord
+ * Selection Renderer support
+ *
+ * Revision 1.26 2001/02/19 17:44:37 lord
+ * Import sort
+ *
+ * Revision 1.25 2001/01/31 17:59:08 lord
+ * Fixed horrible rendering bug. Essentially it was drawing in the wrong
+ * place. Nasty
+ *
+ * Revision 1.24 2001/01/19 19:52:04 lord
+ * Improved the mouse handling. Produces many fewer events now during selection
+ *
+ * Revision 1.23 2001/01/15 18:48:25 lord
+ * Mouse-2 selection handling
+ *
+ * Revision 1.22 2000/12/20 16:47:17 jns
+ * o code added to deal with readonly state of the JAlignmentViewer -
+ * basically as a quick fix it (un)installs the mouse motion listeners.
+ *
+ * Revision 1.21 2000/12/14 17:07:26 jns
+ * o added code to prevent a bug of gap insertion slipage.
+ *
+ * Revision 1.20 2000/12/11 17:25:32 jns
+ * o bug-fix: there was a bug that happened when opening gaps using the
+ * mouse - basically any vertical movement of the mouse was taken into
+ * account, and as a consequence gaps were not always inserted into the
+ * sequence intended. This is now fixed, simply by storing the Y location
+ * of the mouse when the mouse button is pressed, and this being used to
+ * keep track of the sequence the gaps are being opened in.
+ *
+ * Revision 1.19 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.18 2000/11/13 18:20:32 jns
+ * o hopefully this UI now takes account of insets, and therefore draws
+ * itself properly.
+ *
+ * Revision 1.17 2000/11/09 16:21:08 lord
+ * Qualified inner class this calls because jikes complains otherwise
+ *
+ * Revision 1.16 2000/11/03 18:52:10 lord
+ * Blinking cursor installed
+ *
+ * Revision 1.15 2000/11/02 16:35:04 jns
+ * o bug fixing so that it delete's insets properly
+ *
+ * Revision 1.14 2000/11/02 14:57:38 jns
+ * o put in mouse drag stuff
+ * o changed key for deleting residue to more logical DEL key
+ *
+ * Revision 1.13 2000/10/26 17:21:27 jns
+ * o added mouse click to move cursor
+ *
+ * Revision 1.12 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.11 2000/09/27 16:20:22 jns
+ * o reverted back to single fast cell renderer, because of the ability
+ * to generate a multiplexer cell renderer that will render multiple cell
+ * renderers at one time.
+ *
+ * Revision 1.10 2000/09/18 18:03:59 jns
+ * o changes to support multiple cell renderers and drawing them one after another,
+ * on top of each other.
+ * o NB: Therefore, the order of the renderers *is* important - the first renderer
+ * is used first, and all subsequent ones draw over it!
+ *
+ * Revision 1.9 2000/08/01 17:13:41 lord
+ * Now shows the same bit of the alignment if the CellHeight or Width is
+ * shown. This requires scrolling to the new region showing this. At the
+ * moment this makes the screen jump a little, but I'm not sure that its
+ * worth the effort to fix this cosmetic problem.
+ *
+ * Revision 1.8 2000/07/18 11:09:45 lord
+ * Import rationalisation.
+ *
+ * Revision 1.7 2000/06/13 11:12:22 lord
+ * Fixed getLength/getGappedLength bug.
+ *
+ * Revision 1.6 2000/06/05 14:23:50 lord
+ * Fixed bug, now showing last sequence as well
+ *
+ * Revision 1.5 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.4 2000/05/24 15:40:34 lord
+ * Minor algorithmic fiddling. Probably need to rewrite the paint
+ * algorithm here.
+ *
+ * Revision 1.3 2000/05/18 17:06:05 lord
+ * Fixed bug with display of gapped sequences
+ *
+ * Revision 1.2 2000/05/08 17:05:13 lord
+ * Redraws entire viewable area now, even if off the bottom
+ * of the sequence. This seems to make it work better with the
+ * performance speed ups that we are using
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.14 2000/04/18 17:32:28 lord
+ * Modified to take Fast renderer as well as normal one
+ *
+ * Revision 1.13 2000/04/13 12:46:47 lord
+ * Support for selection
+ *
+ * Revision 1.12 2000/04/12 13:42:49 jns
+ * o added in color mapping code
+ *
+ * Revision 1.11 2000/04/11 17:17:35 lord
+ * Elementary selection support added. Probably buggy at the moment
+ *
+ * Revision 1.10 2000/04/06 15:46:25 lord
+ * Changes to support a cursor, with proper cursor movement
+ *
+ * Revision 1.9 2000/04/03 13:54:53 lord
+ * Fixed various sizing bugs
+ *
+ * Revision 1.8 2000/03/31 16:26:58 lord
+ * Removed the links to JAlignmentRuler, and its drawing. Also have
+ * changed the CellRenderer iteration code as it was drawing an extra
+ * cell at the edges that it shouldnt be.
+ *
+ * Revision 1.7 2000/03/29 15:50:47 lord
+ * Updated to use new sequence.geom package
+ *
+ * Revision 1.6 2000/03/29 14:58:51 lord
+ * Should now be able to cope with a null ruler, though I havent actually
+ * tested it out yet.
+ *
+ * Revision 1.5 2000/03/27 18:51:24 lord
+ * Added initial support for JAlignmentRuler
+ *
+ * Revision 1.4 2000/03/23 19:50:42 lord
+ * Unwound for loops for efficiency of drawing
+ *
+ * Revision 1.3 2000/03/21 18:52:47 lord
+ * Now copes with insets, removed hack element
+ *
+ * Revision 1.2 2000/03/21 13:42:06 lord
+ * Lots of changes. Have basic system set up
+ *
+ * Revision 1.1 2000/03/16 16:19:20 lord
+ * Initial checkin
+ *
+ */
+
+
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.java b/src/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.java
new file mode 100644
index 0000000..0b6c41d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/plaf/MetalAlignmentViewerUI.java
@@ -0,0 +1,61 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.plaf; // Package name inserted by JPack
+
+
+/**
+ * MetalAlignmentViewerUI.java
+ *
+ *
+ * Created: Tue Mar 14 16:32:29 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: MetalAlignmentViewerUI.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class MetalAlignmentViewerUI extends BasicAlignmentViewerUI
+{
+
+} // MetalAlignmentViewerUI
+
+
+
+/*
+ * ChangeLog
+ * $Log: MetalAlignmentViewerUI.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.1 2000/03/16 16:19:20 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.java b/src/uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.java
new file mode 100644
index 0000000..af5cdca
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/AlignmentViewerTest.java
@@ -0,0 +1,355 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.test; // Package name inserted by JPack
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.Dictionary;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JMenuBar;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import uk.ac.man.bioinf.gui.color.IndividualElementColorMap;
+import uk.ac.man.bioinf.gui.viewer.Install;
+import uk.ac.man.bioinf.gui.viewer.InvertedScrollPaneLayout;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentRuler;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentViewer;
+import uk.ac.man.bioinf.gui.viewer.JChangedScrollPane;
+import uk.ac.man.bioinf.gui.viewer.plaf.BasicAlignmentViewerUI;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * AlignmentViewerTest.java
+ *
+ *
+ * Created: Wed Mar 15 20:11:02 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentViewerTest.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentViewerTest extends JFrame
+{
+
+ JMenuItem blinkOn, blinkOff;
+ JAlignmentViewer viewer;
+
+ public AlignmentViewerTest() throws Throwable
+ {
+ super( "Test" );
+ Class waste = Install.class;
+
+ addWindowListener
+ ( new WindowAdapter(){
+ public void windowClosing( WindowEvent event )
+ {
+ System.exit( 0 );
+ }
+ });
+
+
+ Element[][] elems = new Element[ 40 ][];
+ elems[ 0 ] = AminoAcid.getAll();
+ elems[ 1 ] = AminoAcid.getAll();
+ elems[ 2 ] = AminoAcid.getAll();
+ elems[ 3 ] = AminoAcid.getAll();
+ elems[ 4 ] = AminoAcid.getAll();
+ elems[ 5 ] = AminoAcid.getAll();
+ elems[ 6 ] = AminoAcid.getAll();
+ elems[ 7 ] = AminoAcid.getAll();
+ elems[ 8 ] = AminoAcid.getAll();
+ elems[ 9 ] = AminoAcid.getAll();
+ elems[ 10 ] = AminoAcid.getAll();
+ elems[ 11 ] = AminoAcid.getAll();
+ elems[ 12 ] = AminoAcid.getAll();
+ elems[ 13 ] = AminoAcid.getAll();
+ elems[ 14 ] = AminoAcid.getAll();
+ elems[ 15 ] = AminoAcid.getAll();
+ elems[ 16 ] = AminoAcid.getAll();
+ elems[ 17 ] = AminoAcid.getAll();
+ elems[ 18 ] = AminoAcid.getAll();
+ elems[ 19 ] = AminoAcid.getAll();
+ elems[ 20 ] = AminoAcid.getAll();
+ elems[ 21 ] = AminoAcid.getAll();
+ elems[ 22 ] = AminoAcid.getAll();
+ elems[ 23 ] = AminoAcid.getAll();
+ elems[ 24 ] = AminoAcid.getAll();
+ elems[ 25 ] = AminoAcid.getAll();
+ elems[ 26 ] = AminoAcid.getAll();
+ elems[ 27 ] = AminoAcid.getAll();
+ elems[ 28 ] = AminoAcid.getAll();
+ elems[ 29 ] = AminoAcid.getAll();
+ elems[ 30 ] = AminoAcid.getAll();
+ elems[ 31 ] = AminoAcid.getAll();
+ elems[ 32 ] = AminoAcid.getAll();
+ elems[ 33 ] = AminoAcid.getAll();
+ elems[ 34 ] = AminoAcid.getAll();
+ elems[ 35 ] = AminoAcid.getAll();
+ elems[ 36 ] = AminoAcid.getAll();
+ elems[ 37 ] = AminoAcid.getAll();
+ elems[ 38 ] = AminoAcid.getAll();
+ elems[ 39 ] = AminoAcid.getAll();
+
+ DefaultSequenceAlignment msa = new DefaultSequenceAlignment( elems, ProteinSequenceType.getInstance() );
+ msa.setInset( 3, 13 );
+ msa.setInset( 1, 6 );
+ msa.setInset( 4, 8 );
+ msa.setInset( 2, 4 );
+ msa.setInset( 5, 43 );
+ msa.setInset( 6, 1 );
+ msa.setInset( 7, 5 );
+ msa.setInset( 8, 0 );
+ msa.setInset( 9, 6 );
+ msa.setInset( 10, 13 );
+ msa.setInset( 13, 3 );
+ msa.setInset( 11, 6 );
+ msa.setInset( 14, 38 );
+ msa.setInset( 12, 4 );
+ msa.setInset( 15, 9 );
+ msa.setInset( 16, 1 );
+ msa.setInset( 17, 5 );
+ msa.setInset( 18, 0 );
+ msa.setInset( 19, 6 );
+ msa.setInset( 20, 3 );
+ msa.setInset( 23, 3 );
+ msa.setInset( 21, 6 );
+ msa.setInset( 24, 8 );
+ msa.setInset( 22, 4 );
+ msa.setInset( 25, 9 );
+ msa.setInset( 26, 1 );
+ msa.setInset( 27, 5 );
+ msa.setInset( 28, 0 );
+ msa.setInset( 29, 6 );
+ msa.setInset( 30, 3 );
+ msa.setInset( 33, 3 );
+ msa.setInset( 31, 6 );
+ msa.setInset( 34, 8 );
+ msa.setInset( 32, 4 );
+ msa.setInset( 35, 9 );
+ msa.setInset( 36, 1 );
+ msa.setInset( 37, 5 );
+ msa.setInset( 38, 0 );
+ msa.setInset( 39, 6 );
+ msa.setInset( 40, 3 );
+
+ // color mapping
+ AminoAcid[] aa = AminoAcid.getAll();
+ Color[] colors = new Color[aa.length];
+ for (int i = 0; i < colors.length; i++) {
+ if (aa[i] == AminoAcid.GLYCINE)
+ colors[i] = new Color(255, 170, 136);
+ else if (aa[i] == AminoAcid.ALANINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.VALINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.LEUCINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.ISOLEUCINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.SERINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.CYSTEINE)
+ colors[i] = new Color(255, 255, 136);
+ else if (aa[i] == AminoAcid.THREONINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.METHIONINE)
+ colors[i] = new Color(255, 255, 255);
+ else if (aa[i] == AminoAcid.PHENYLALANINE)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.TYROSINE)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.TRYPTOPHAN)
+ colors[i] = new Color(255, 136, 255);
+ else if (aa[i] == AminoAcid.PROLINE)
+ colors[i] = new Color(255, 170, 136);
+ else if (aa[i] == AminoAcid.HISTIDINE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.LYSINE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.ARGININE)
+ colors[i] = new Color(136, 255, 255);
+ else if (aa[i] == AminoAcid.ASPARTICACID)
+ colors[i] = new Color(255, 136, 136);
+ else if (aa[i] == AminoAcid.GLUTAMICACID)
+ colors[i] = new Color(255, 136, 136);
+ else if (aa[i] == AminoAcid.ASPARAGINE)
+ colors[i] = new Color(136, 255, 136);
+ else if (aa[i] == AminoAcid.GLUTAMINE)
+ colors[i] = new Color(136, 255, 136);
+ else
+ colors[i] = new Color(102, 102, 102);
+ }
+ IndividualElementColorMap cm = new IndividualElementColorMap("test", elems[0], colors);
+
+ System.out.println( "Amino acid " + ((Object[])AminoAcid.getAll()).length );
+
+ System.out.println( "The length of the msa is " + msa.getLength() );
+ //JLabel viewer = new JLabel( "Viewer Label " );
+
+ viewer = new JAlignmentViewer( msa );
+ viewer.setCellWidth( 40 );
+ viewer.setCellHeight( 40 );
+ viewer.setColorMap(cm); // set the color map for the viewer
+
+ JChangedScrollPane pane = new JChangedScrollPane
+ ( new InvertedScrollPaneLayout(),
+ viewer,
+ JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED );
+ // performance speed ups
+ System.out.println( "Backing store enabled" );
+ pane.getViewport().setBackingStoreEnabled( true );
+ System.out.println( "Window blitting" );
+ pane.getViewport().putClientProperty
+ ("EnableWindowBlit", Boolean.TRUE);
+
+ // this prevents the scroll pane from resizing the JAlignmentRuler
+ // in a manner I consider to be wrong!!!
+ JPanel rulerPanel = new JPanel();
+ rulerPanel.setLayout( new BorderLayout() );
+
+ JAlignmentRuler ruler = new JAlignmentRuler( msa );
+
+ ruler.setPreferredWidthPerBase( viewer.getCellWidth() );
+ pane.setColumnHeaderView( rulerPanel );
+
+ Dictionary dic = ruler.getLabelTable();
+ JLabel oneLabel = (JLabel)dic.get( new Integer( 1 ) );
+ oneLabel.setText( " 1" );
+ ruler.setLabelTable( dic );
+
+
+ rulerPanel.add( ruler, BorderLayout.WEST );
+
+ JMenuBar bar;
+
+ setJMenuBar( bar = new JMenuBar() );
+
+ bar.add( blinkOn = new JMenuItem( "ON" ) );
+ blinkOn.addActionListener
+ ( new ActionListener(){
+ public void actionPerformed( ActionEvent event )
+ {
+ BasicAlignmentViewerUI ui =
+ (BasicAlignmentViewerUI)AlignmentViewerTest.this.viewer.getAlignmentUI();
+ ui.setCursorBlink();
+ }
+ });
+ bar.add( blinkOff = new JMenuItem( "OFF" ) );
+ blinkOff.addActionListener
+ ( new ActionListener() {
+ public void actionPerformed( ActionEvent event )
+ {
+ BasicAlignmentViewerUI ui =
+ (BasicAlignmentViewerUI)AlignmentViewerTest.this.viewer.getAlignmentUI();
+ ui.unsetCursorBlink();
+ }
+ });
+
+
+ pane.setSize( 400, 400 );
+ getContentPane().add( pane );
+ setSize( 400, 400 );
+ viewer.setVisible( true );
+ System.out.println( "Calling set visible ");
+ setVisible( true );
+
+
+ }
+
+ public static void main( String[] args ) throws Throwable
+ {
+ AlignmentViewerTest test = new AlignmentViewerTest();
+
+ } //end main method
+
+} // AlignmentViewerTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentViewerTest.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.4 2000/04/20 13:59:01 lord
+ * Lots of tedious changes
+ *
+ * Revision 1.3 2000/04/18 18:07:49 jns
+ * o modified to allow for Element, which remains in the sequence pacakge, not the types package.
+ *
+ * Revision 1.2 2000/04/18 18:00:14 lord
+ * Modified to reflect changed package names
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ * Revision 1.8 2000/04/18 17:33:26 lord
+ * Various blitting methods tried out
+ *
+ * Revision 1.7 2000/04/12 13:43:00 jns
+ * o added in color mapping code
+ *
+ * Revision 1.6 2000/04/03 13:55:12 lord
+ * Lots of tedious changes
+ *
+ * Revision 1.5 2000/03/31 16:27:39 lord
+ * Made a series of changes to cope with the movement of the
+ * JAlignmentRuler out of the JAlignmentViewer class
+ *
+ * Revision 1.4 2000/03/29 14:59:16 lord
+ * Various unexciting changes
+ *
+ * Revision 1.3 2000/03/21 18:52:07 lord
+ * More tedious changes
+ *
+ * Revision 1.2 2000/03/21 13:42:31 lord
+ * Changes to boring to document
+ *
+ * Revision 1.1 2000/03/16 16:19:20 lord
+ * Initial checkin
+ *
+ */
+
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.java b/src/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.java
new file mode 100644
index 0000000..00d8a3c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/BasicWindowMonitor.java
@@ -0,0 +1,30 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.viewer.test; // Package name inserted by JPack
+
+import java.awt.event.*;
+import java.awt.Window;
+
+public class BasicWindowMonitor extends WindowAdapter {
+
+ public void windowClosing(WindowEvent e) {
+ Window w = e.getWindow();
+ w.setVisible(false);
+ w.dispose();
+ System.exit(0);
+ }
+}
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.java b/src/uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.java
new file mode 100644
index 0000000..09c67b0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/ButtonPanelTest.java
@@ -0,0 +1,87 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.test; // Package name inserted by JPack
+
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import javax.swing.JFrame;
+import javax.swing.JScrollPane;
+import uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentButtonPanel;
+
+
+/**
+ * ButtonPanelTest.java
+ *
+ *
+ * Created: Fri May 19 17:22:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ButtonPanelTest.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ButtonPanelTest implements ItemListener
+{
+ public static void main( String[] args ) throws Throwable
+ {
+ JFrame frame = new JFrame( "Test" );
+
+ JAlignmentButtonPanel panel = new JAlignmentButtonPanel( CinemaTestLaunch.generateMsa() );
+ JScrollPane scrollPane = new JScrollPane( panel );
+
+ frame.getContentPane().add
+ ( scrollPane );
+ panel.addItemListener( new ButtonPanelTest() );
+ frame.setSize( 300, 100 );
+ frame.setVisible( true );
+ } //end main method
+
+ public void itemStateChanged( ItemEvent event )
+ {
+ System.out.println( event.getItem() + " " + ((Sequence)event.getItem()).getIdentifier().getTitle() );
+ }
+
+} // ButtonPanelTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: ButtonPanelTest.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/07/18 11:10:00 lord
+ * Import rationalisation.
+ * Changes due to removal of biointerface
+ *
+ * Revision 1.1 2000/05/24 15:40:50 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.java b/src/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.java
new file mode 100644
index 0000000..8e0cb61
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/CellRendererPaneReplacement.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.test; // Package name inserted by JPack
+import javax.swing.CellRendererPane;
+import java.awt.Graphics;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Color;
+import javax.swing.JComponent;
+//import javax.swing.SwingGraphics;
+
+
+/**
+ * CellRendererPaneReplacement.java
+ *
+ *
+ * Created: Fri Apr 14 17:02:05 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CellRendererPaneReplacement.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class CellRendererPaneReplacement extends CellRendererPane
+{
+
+ public void paintComponent(Graphics g, Component c, Container p,
+ int x, int y, int w, int h, boolean shouldValidate) {
+ if (c == null) {
+ if (p != null) {
+ Color oldColor = g.getColor();
+ g.setColor(p.getBackground());
+ g.fillRect(x, y, w, h);
+ g.setColor(oldColor);
+ }
+ return;
+ }
+
+ if (c.getParent() != this) {
+ this.add(c);
+ }
+
+ c.setBounds(x, y, w, h);
+
+ if(shouldValidate) {
+ c.validate();
+ }
+
+ boolean wasDoubleBuffered = false;
+ if ((c instanceof JComponent) && ((JComponent)c).isDoubleBuffered()) {
+ wasDoubleBuffered = true;
+ ((JComponent)c).setDoubleBuffered(false);
+ }
+
+ // move the co-ord space
+ g.translate( x, y );
+ c.paint(g);
+ // and move it back
+ g.translate( -x, - y);
+
+
+ if ((c instanceof JComponent) && wasDoubleBuffered) {
+ ((JComponent)c).setDoubleBuffered(true);
+ }
+
+ // this bit is a buggy (4204449) duplication and can safely
+ // be deleted
+
+ // if (c instanceof JComponent) {
+// JComponent jc = (JComponent)c;
+// jc.setDoubleBuffered(wasDoubleBuffered);
+// }
+
+ c.setBounds(-w, -h, 0, 0);
+ }
+
+} // CellRendererPaneReplacement
+
+
+
+/*
+ * ChangeLog
+ * $Log: CellRendererPaneReplacement.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/Makefile b/src/uk/ac/man/bioinf/gui/viewer/test/Makefile
new file mode 100644
index 0000000..3e7fb9f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/Makefile
@@ -0,0 +1,73 @@
+####
+#### Java Makefile automatically generated by jmaker 1.17
+#### Creation date: Sat Apr 1 18:31:03 2000
+####
+
+#### Use bash. sh seems to no expand ~ properlySHELL = /bin/bash
+
+####settings for alternate packages directory
+PACKAGE_DIRECTORY = /mobilehome/phil/java/packages/uk/ac/man/bioinf/viewer/test/
+vpath %.class $(PACKAGE_DIRECTORY)
+
+#### this is a short hand for what we want to set the compiler to. It
+COMP = default
+JAVAC = javac
+CLASSPATH = /mobilehome/phil/java/packages:/usr/lib/java/blackdown/jdk1.2.2rc4/jre/lib/rt.jar
+JAVAC_FLAGS = -d $(PACKAGE_DIRECTORY)
+
+####Compiler settings for jikes
+JIKES = jikes
+JIKES_CORE_CLASSPATH = /usr/lib/java/blackdown/jdk1.2.2rc4/jre/lib/rt.jar
+
+####Settings for using blackdown resources
+BLACKDOWN_JAVAC = /usr/lib/java/blackdown/jdk1.2.2rc4/bin/javac
+
+####Settings for using sun resources
+SUN_JAVAC = /usr/lib/java/sun/jdk1.2.2rc2/bin/javac
+
+####set up the variables appropriately
+ifeq "$(COMP)" "jikes"
+JAVAC := $(JIKES)
+CLASSPATH := $(CLASSPATH):$(JIKES_CORE_CLASSPATH)
+JAVAC_FLAGS:= $(JAVAC_FLAGS) +E
+endif
+ifeq "$(COMP)" "sun"
+JAVAC := $(SUN_JAVAC)
+endif
+
+ifeq "$(COMP)" "black"
+JAVAC := $(BLACKDOWN_JAVAC)
+endif
+
+#### Build Rules
+%.class: %.java
+ $(JAVAC) $(JAVAC_FLAGS) $<
+
+#### Global target
+all: \
+ AlignmentViewerTest \
+ BasicWindowMonitor \
+ SliderExample
+
+#### Single targets
+AlignmentViewerTest: AlignmentViewerTest.class
+BasicWindowMonitor: BasicWindowMonitor.class
+SliderExample: SliderExample.class
+
+#### Cleanup
+clean:
+ifdef PACKAGE_DIRECTORY cd $(PACKAGE_DIRECTORY);$(RM) *.classelse $(RM) *.class
+endif
+#### Rebuild
+build: clean all
+
+#### Usage
+help:
+ @echo "Usage: make [all|<single target>|clean|build|help]"
+ @echo " all - build all as needed (default)"
+ @echo " <single target> - build the given file as needed"
+ @echo " clean - remove all .class files"
+ @echo " build - build all inconditionnally"
+ @echo " help - display this help"
+ @echo " Use COMP=sun,black,jikes as appropriate"
+
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.java b/src/uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.java
new file mode 100644
index 0000000..30ef4c2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/SingleSelectionModelTest.java
@@ -0,0 +1,71 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.gui.viewer.test; // Package name inserted by JPack
+import java.awt.Rectangle;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+
+
+/**
+ * SingleSelectionModelTest.java
+ *
+ *
+ * Created: Wed Apr 12 17:34:46 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SingleSelectionModelTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SingleSelectionModelTest
+{
+ public static void main( String[] args )
+ {
+ Rectangle rect = new Rectangle( 5, 4, 0, 0 );
+ rect.add( 2, 2 );
+ System.out.println( rect );
+
+ SequenceAlignmentRectangle seqRect = new SequenceAlignmentRectangle( 5, 4, 0, 0 );
+ seqRect.add( 2, 2 );
+ System.out.println( seqRect );
+
+
+ } //end main method
+} // SingleSelectionModelTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: SingleSelectionModelTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:45:24 lord
+ * All files moved from uk.ac.man.bioinf.viewer package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/gui/viewer/test/SliderExample.java b/src/uk/ac/man/bioinf/gui/viewer/test/SliderExample.java
new file mode 100644
index 0000000..7643c3f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/gui/viewer/test/SliderExample.java
@@ -0,0 +1,56 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.gui.viewer.test; // Package name inserted by JPack
+// SliderExample.java
+//
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.border.*;
+import uk.ac.man.bioinf.gui.viewer.Install;
+import uk.ac.man.bioinf.gui.viewer.JAlignmentRuler;
+
+public class SliderExample extends JPanel {
+
+ public SliderExample() {
+
+ super(true);
+
+ this.setLayout(new BorderLayout());
+ JAlignmentRuler slider = new JAlignmentRuler();
+ slider.setMinorTickSpacing(2);
+ slider.setMajorTickSpacing(10);
+ slider.setPaintTicks(true);
+ slider.setPaintLabels(true);
+
+ // Note that the following line is really unnecessary. By setting a
+ // positive integer to the major tick spacing and setting the paintLabel
+ // property to true, it's done for us!
+
+ slider.setLabelTable(slider.createStandardLabels(10));
+ add(slider, BorderLayout.CENTER);
+ }
+
+ public static void main(String s[]) {
+ Class cla = Install.class;
+ JFrame frame = new JFrame("Slider");
+ frame.addWindowListener(new BasicWindowMonitor());
+ frame.setContentPane(new SliderExample());
+ frame.pack();
+ frame.setVisible(true);
+ }
+}
diff --git a/src/uk/ac/man/bioinf/io/AlignmentInputParser.java b/src/uk/ac/man/bioinf/io/AlignmentInputParser.java
new file mode 100644
index 0000000..893ce99
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/AlignmentInputParser.java
@@ -0,0 +1,109 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+import java.io.IOException;
+import java.io.Reader;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+/**
+ * This is an interface that provides a definition for any sequence
+ * parsers. It takes input and returns a sequence alignment
+ * object. Parsers may <b>or</b> may not have state attached to
+ * them. Furthermore they may be re-entered <b>or</b> alternatively
+ * they may not. You have been warned.
+ * <p>
+ * One thing which cannot be enforced in the interface is that every
+ * parser should have a default constructor (ie no arguments to the
+ * constructor). This is because the parsers are generated through
+ * Class.newInstance().
+ *
+ *
+ * Created: Thu May 25 23:01:02 2000
+ *
+ * @author Julian
+ * @version $Id: AlignmentInputParser.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface AlignmentInputParser
+{
+ public SequenceAlignment parse( Identifier ident, Reader reader, ParserExceptionHandler eh )
+ throws IOException;
+
+ /**
+ * This method returns a sequence alignment from a buffered reader
+ * input stream.
+ *
+ * @param reader the input stream
+ * @param eh exception handler
+ * @return the sequence alignment
+ */
+ public SequenceAlignment parse(Reader reader, ParserExceptionHandler eh)
+ throws IOException;
+
+ /**
+ * Returns the description of this alignment parser, and should be
+ * human readable/understandable.
+ *
+ * @return the description
+ */
+ public String getDescription();
+}// AlignmentInputParser
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentInputParser.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/09/11 13:19:26 lord
+ * Added identifier support
+ *
+ * Revision 1.2 2000/08/01 14:57:46 jns
+ * o removal of BioInterface
+ *
+ * Revision 1.1 2000/07/27 22:02:40 jns
+ * o mv from AlignmentParser because will now have output parsers as well
+ * o rm the extends BioInterface as this is becoming extinct - Phil did one
+ * end of this, but not here - so...
+ *
+ * Revision 1.3 2000/06/16 09:37:10 jns
+ * o added a getDescription() method for a human readable form of
+ * what the parser is.
+ *
+ * Revision 1.2 2000/06/08 21:14:08 jns
+ * o removed toSequence function as it defined implementation.
+ * o consequently added an exception handler to the parse method.
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/AlignmentOutputParser.java b/src/uk/ac/man/bioinf/io/AlignmentOutputParser.java
new file mode 100644
index 0000000..907cfca
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/AlignmentOutputParser.java
@@ -0,0 +1,89 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+import java.io.Writer;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+/**
+ * This is an interface that provides a definition for any sequence
+ * output parsing. It takes a sequence alignment and returns a
+ * writer. Parsers may <b>or</b> may not have state attached to them,
+ * and furthermore, they may be re-entered <b>or</b> alternately they
+ * may not. You have been warned!
+ * <p>
+ * One thing that cannot be enforced in the interface is, every parser
+ * should have a default constructor (i.e., no arguments to the
+ * constructor). This is because the parsers are generated through
+ * Class.newInstance().
+ *
+ *
+ * Created: Mon Jul 31 13:04:06 2000
+ *
+ * @author Julian Selley
+ * @version $Id: AlignmentOutputParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface AlignmentOutputParser
+{
+ /**
+ * Returns a writer for output, when provided with a sequence
+ * alignment. Exceptions are handled by the supplied exception
+ * handler.
+ *
+ * @param sa the sequence alignment
+ * @param eh the exception handler
+ * @return the writer for output
+ */
+ public Writer write(SequenceAlignment sa, Writer writer, ParserExceptionHandler eh);
+
+ /**
+ * Returns the description of this alignment output parser, and
+ * should be human readable/understandable.
+ *
+ * @return the description
+ */
+ public String getDescription();
+}// AlignmentOutputParser
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentOutputParser.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/31 18:02:26 lord
+ * Now returns the writer, rather than void. Largely because it can.
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.java b/src/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.java
new file mode 100644
index 0000000..baf2ad7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/DefaultParserExceptionHandler.java
@@ -0,0 +1,73 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+
+/**
+ * This parser exception handler does very little.
+ *
+ *
+ * Created: Sat Jun 3 18:14:01 2000
+ *
+ * @author Julian Selley
+ * @version $Id: DefaultParserExceptionHandler.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultParserExceptionHandler
+ implements ParserExceptionHandler
+{
+ public DefaultParserExceptionHandler() {}
+
+ public void handleException(ParserException e)
+ {
+ if (e.getMessage() != null)
+ System.err.println(e.getMessage());
+ throw e;
+ }
+} // DefaultParserExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultParserExceptionHandler.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/07/27 22:04:37 jns
+ * o rm the extends BioObject as this is being retired for a newer and better
+ * system, as yet unrevieled
+ * o added to deal with ParserException rather than ParseException - I felt
+ * this was a better name as I invariably forgot when we were dealing with
+ * ParseExceptions and when we were dealing with ParserExceptionHandlers.
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.java b/src/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.java
new file mode 100644
index 0000000..4d0868e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/InvalidSequenceTypeParserException.java
@@ -0,0 +1,96 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.SequenceType;
+
+
+/**
+ * This exception is cast when there is a mismatch of sequence types
+ * when dealing with parsers.
+ *
+ *
+ * Created: Tue Aug 8 12:32:18 2000
+ *
+ * @author Julian Selley
+ * @version $Id: InvalidSequenceTypeParserException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class InvalidSequenceTypeParserException extends ParserException
+{
+ private SequenceType expectedSequenceType;
+
+ public InvalidSequenceTypeParserException()
+ {
+ super("A mismatch of sequence types has occurred!", -1);
+ }
+
+ public InvalidSequenceTypeParserException(String message)
+ {
+ super(message, -1);
+ }
+
+ public InvalidSequenceTypeParserException(SequenceType st)
+ {
+ super("A mismatch of sequence types has occurred! " +
+ st.getName() + " was the expected type.", -1);
+ this.expectedSequenceType = st;
+ }
+
+ public InvalidSequenceTypeParserException(String message, SequenceType st)
+ {
+ super(message, -1);
+ this.expectedSequenceType = st;
+ }
+
+ /**
+ * Returns the expected sequence type.
+ *
+ * @return
+ */
+ public SequenceType getExpcetedSequenceType()
+ {
+ return this.expectedSequenceType;
+ }
+} // InvalidSequenceTypeException
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvalidSequenceTypeParserException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/22 17:10:19 lord
+ * Created due to name clash of InvalidSequenceTypeException
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/NarrowedInputStream.java b/src/uk/ac/man/bioinf/io/NarrowedInputStream.java
new file mode 100644
index 0000000..85dc349
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/NarrowedInputStream.java
@@ -0,0 +1,222 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PushbackInputStream;
+
+
+/**
+ * NarrowedInputStream.java
+ *
+ * This InputStream wraps another and puts a limits access to that
+ * stream. It hides all of the input that occur before the first
+ * occurrence of a given input, and ends after the occurrence of the
+ * second.
+ *
+ * It may well be useful in a number of circumstances, but it should
+ * be particularly good for pulling out data from the middle of an
+ * HTML page between two tags.
+ *
+ * Created: Thu Feb 8 17:39:21 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: NarrowedInputStream.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NarrowedInputStream extends InputStream
+{
+
+ private PushbackInputStream push;
+ private byte[] start, stop;
+ private boolean beforeStart = true;
+ private boolean afterEnd = false;
+ private boolean markStart = false;
+ private int markLimit;
+ private byte[] comprStart;
+ private byte[] comprEnd;
+
+
+ public NarrowedInputStream( InputStream stream, byte[] start, byte[] stop )
+ {
+ // blargh
+ super();
+ this.push = new PushbackInputStream
+ (( new NoisyStream( stream ) ),
+ Math.max
+ ( ((start == null ) ? 0 : start.length),
+ ((stop == null ) ? 0 : stop.length ) ));
+
+ this.start = start;
+ this.stop = stop;
+ if( start != null )
+ this.comprStart = new byte[ start.length ];
+ if( stop != null )
+ this.comprEnd = new byte[ stop.length ];
+ }
+
+ class NoisyStream extends InputStream
+ {
+ InputStream inp;
+ public NoisyStream( InputStream inp )
+ {
+ this.inp = inp;
+ }
+
+ public int read() throws IOException
+ {
+ int retn = inp.read();
+ System.out.print( (char)retn );
+ return retn;
+ }
+
+ public int read( byte[] b ) throws IOException
+ {
+ int retn = inp.read( b );
+ System.out.println( "String is " + new String( b ) );
+ return retn;
+ }
+ }
+
+
+
+ private void readToStart() throws IOException
+ {
+
+ boolean cont = true;
+
+ if( start == null ){
+ cont = false;
+ beforeStart = false;
+ }
+
+ while( cont ){
+ // read some bytes
+ int val = push.read( comprStart );
+ //System.out.print( (char)comprStart[ 0 ] + " " );
+ try{
+ Thread.sleep( 5 );
+ }
+ catch( InterruptedException ie ){
+ }
+
+ // if cont -1 we have reached the end of the stream before the
+ // start
+ if( val == -1 ){
+ afterEnd = true;
+ cont = false;
+ }else{
+ if( compareArrays( start, comprStart ) ){
+ // we have now reached the start of the stream, so we have
+ // read up to the right point.
+ cont = false;
+ beforeStart = false;
+ }
+ else{
+ // we have not read up to the right point therefore we want to
+ // push back everything but the first byte.
+ push.unread( comprStart, 1, comprStart.length - 1 );
+ }
+ }
+ }
+
+ // if mark has already been called then it must have been on the
+ // right at the beginning of the stream, which is now, rather than
+ // the start of the internal stream.
+ if( markStart ) super.mark( markLimit );
+ }
+
+ /**
+ * Compare two arrays.
+ * @param fixed the fixed array, ie either the start or stop array
+ * @param notFixed the other array to compare.
+ * @return true if they are the same.
+ */
+ private boolean compareArrays( byte[] fixed, byte[] notFixed )
+ {
+ for( int i = 0; i < fixed.length; i++ ){
+ if( fixed[ i ] != notFixed[ i ] ){
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public int read() throws IOException
+ {
+ // have we started yet?
+ if( beforeStart ) readToStart();
+
+ // do we want to stop?
+ if( stop == null ){
+ return push.read();
+ }
+
+ // have we finished yet?
+ if( afterEnd ) return -1;
+
+ // read the enough bytes to check that we have not reached the
+ // end.
+ push.read( comprEnd, 0 , comprEnd.length );
+
+ // we have reached the end.
+ if( compareArrays( stop, comprEnd ) ){
+ afterEnd = true;
+ return -1;
+ }
+
+ // push back all put the first
+ push.unread( comprEnd, 1, comprEnd.length - 1 );
+ return comprEnd[ 0 ];
+ }
+
+ public void mark( int readlimit )
+ {
+ if( beforeStart ){
+ markStart = true;
+ markLimit = readlimit;
+ }
+ else{
+ super.mark( readlimit );
+ }
+ }
+}// NarrowedInputStream
+
+
+
+/*
+ * ChangeLog
+ * $Log: NarrowedInputStream.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:45:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/NullParserExceptionHandler.java b/src/uk/ac/man/bioinf/io/NullParserExceptionHandler.java
new file mode 100644
index 0000000..ce90c8c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/NullParserExceptionHandler.java
@@ -0,0 +1,83 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+import java.io.PrintStream;
+import java.io.PrintWriter;
+
+
+/**
+ * NullParserExceptionHandler.java
+ *
+ * An exception handler for all seasons
+ *
+ * Created: Thu Feb 8 21:24:57 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: NullParserExceptionHandler.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NullParserExceptionHandler implements ParserExceptionHandler
+{
+ private PrintWriter stream = new PrintWriter( System.out );
+ private boolean dumpStack;
+
+ public NullParserExceptionHandler()
+ {
+ this( true );
+ }
+
+ public NullParserExceptionHandler( boolean dumpStack )
+ {
+ this.dumpStack = dumpStack;
+ }
+
+ public NullParserExceptionHandler( PrintWriter stream )
+ {
+ this.stream = stream;
+ this.dumpStack = true;
+ }
+
+ public void handleException( ParserException exp )
+ {
+ if( dumpStack ) exp.printStackTrace( stream );
+ }
+} // NullParserExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: NullParserExceptionHandler.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:45:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/ParserException.java b/src/uk/ac/man/bioinf/io/ParserException.java
new file mode 100644
index 0000000..211fbac
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/ParserException.java
@@ -0,0 +1,137 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * A general exception thrown up when parsing a sequence. The concept
+ * is to make this more specific by sub-classing this exception.
+ *
+ *
+ * Created: Tue Jun 6 18:09:26 2000
+ *
+ * @author J Selley
+ * @version $Id: ParserException.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ParserException extends RuntimeException
+{
+ private int position; // the position of the residue causing the exception
+ private String sequence; // the sequence causing the exception
+ private Identifier identifier; // the sequence identifier - primarily the description
+
+ public ParserException(int i)
+ {
+ super();
+ this.position = i;
+ }
+
+ public ParserException(String message, int i)
+ {
+ super(message);
+ this.position = i;
+ }
+
+ public ParserException(int i, String seq)
+ {
+ super();
+ this.position = i;
+ this.sequence = seq;
+ }
+
+ public ParserException(String message, int i, String seq)
+ {
+ super(message);
+ this.position = i;
+ this.sequence = seq;
+ }
+
+ public ParserException(String message, int i, String seq, Identifier ident)
+ {
+ super(message);
+ this.position = i;
+ this.sequence = seq;
+ this.identifier = ident;
+ }
+
+ /**
+ * Returns the integer position in the sequence that caused the
+ * exception.
+ *
+ * @return the location
+ */
+ public int getPosition()
+ {
+ return this.position;
+ }
+
+ /**
+ * Returns the sequence that caused the exception.
+ *
+ * @return the sequence
+ */
+ public String getSequence()
+ {
+ return this.sequence;
+ }
+
+ public Identifier getIdentifier()
+ {
+ return this.identifier;
+ }
+} // ParserException
+
+
+
+/*
+ * ChangeLog
+ * $Log: ParserException.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/10/13 14:33:23 jns
+ * o sorting out a problem with null elements (X) that I had previously
+ * had working, but I then messed it up trying to be smart. I have sorted
+ * by taking out the actualy formation of the sequence, but supplied the
+ * basic elements for creating the sequence.
+ *
+ * Revision 1.1 2000/07/27 22:06:44 jns
+ * o mv to ParserException from ParseException because I kept getting confused
+ * and this seemed a logical time to make a change.
+ * o added stuff to deal with sequence as well, which I thought might be logical
+ * as my error handling so far was just saying the position and not the sequence
+ * in the alignment.
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/ParserExceptionHandler.java b/src/uk/ac/man/bioinf/io/ParserExceptionHandler.java
new file mode 100644
index 0000000..ff7fe13
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/ParserExceptionHandler.java
@@ -0,0 +1,71 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+
+/**
+ * Handles exceptions generated by any sequence parsers.
+ *
+ *
+ * Created: Sat Jun 3 18:07:14 2000
+ *
+ * @author Julian Selley
+ * @version $Id: ParserExceptionHandler.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ParserExceptionHandler
+{
+ /**
+ * Handles exceptions thrown by a sequence parser.
+ *
+ * @param e the exception
+ */
+ public void handleException(ParserException e);
+}// ParserExceptionHandler
+
+
+/*
+ * ChangeLog
+ * $Log: ParserExceptionHandler.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/07/27 22:07:28 jns
+ * o mv to ParserException - I was getting confused between ParserExceptionHandlers
+ * and ParseExceptions.
+ *
+ * Revision 1.2 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/SequenceInputParser.java b/src/uk/ac/man/bioinf/io/SequenceInputParser.java
new file mode 100644
index 0000000..7b93e81
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/SequenceInputParser.java
@@ -0,0 +1,66 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.Sequence;
+import java.io.Reader;
+import java.io.IOException;
+
+
+/**
+ * SequenceInputParser.java
+ *
+ * This class defines the basic interface for parsing sequence files.
+ *
+ * Created: Wed Feb 7 15:00:38 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceInputParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceInputParser
+{
+ public Sequence parse( Reader reader, ParserExceptionHandler eh )
+ throws IOException;
+
+ public String getDescription();
+} // SequenceInputParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceInputParser.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:45:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/SequenceWriterException.java b/src/uk/ac/man/bioinf/io/SequenceWriterException.java
new file mode 100644
index 0000000..3c74339
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/SequenceWriterException.java
@@ -0,0 +1,62 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+
+/**
+ * An exception cast when an IOException is thrown in writing the
+ * sequence out from CINEMA.
+ *
+ *
+ * Created: Tue Aug 8 18:26:21 2000
+ *
+ * @author Julian Selley
+ * @version $Id: SequenceWriterException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceWriterException extends ParserException
+{
+ public SequenceWriterException()
+ {
+ super("An IOException was thrown when attempting to write the sequence.",
+ -1);
+ }
+} // SequenceWriterException
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceWriterException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/UnknownElementException.java b/src/uk/ac/man/bioinf/io/UnknownElementException.java
new file mode 100644
index 0000000..0783841
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/UnknownElementException.java
@@ -0,0 +1,94 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * An exception to flag an unrecognised element in a string.
+ *
+ *
+ * Created: Wed Jun 7 13:28:11 2000
+ *
+ * @author J Selley
+ * @version $Id: UnknownElementException.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class UnknownElementException extends ParserException
+{
+ public UnknownElementException(int i)
+ {
+ super(i);
+ }
+
+ public UnknownElementException(String message, int i)
+ {
+ super(message, i);
+ }
+
+ public UnknownElementException(int i, String seq)
+ {
+ super(i, seq);
+ }
+
+ public UnknownElementException(String message, int i, String seq)
+ {
+ super(message, i, seq);
+ }
+
+ public UnknownElementException(String message, int i, String seq, Identifier seqIdent)
+ {
+ super(message, i, seq, seqIdent);
+ }
+} // UnknownElementException
+
+
+
+/*
+ * ChangeLog
+ * $Log: UnknownElementException.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/10/13 14:33:23 jns
+ * o sorting out a problem with null elements (X) that I had previously
+ * had working, but I then messed it up trying to be smart. I have sorted
+ * by taking out the actualy formation of the sequence, but supplied the
+ * basic elements for creating the sequence.
+ *
+ * Revision 1.2 2000/07/27 22:09:37 jns
+ * o changed to ParserException as this was mv to new file name
+ * o added stuff to handle sequences as well as just position and message
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.java b/src/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.java
new file mode 100644
index 0000000..421d66d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/parsers/AbstractProteinAlignmentInputParser.java
@@ -0,0 +1,148 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.parsers; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.io.AlignmentInputParser;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.UnknownElementException;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * Provides a function to parse amino acids from the input stream.
+ *
+ *
+ * Created: Fri May 26 12:32:09 2000
+ *
+ * @author J Selley
+ * @version $Id: AbstractProteinAlignmentInputParser.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractProteinAlignmentInputParser
+ implements AlignmentInputParser
+{
+ private static AminoAcid[] aa;
+
+ static
+ {
+ AminoAcid[] all = AminoAcid.getAll();
+ aa = new AminoAcid[26];
+
+ for (int i = 0; i < all.length; i++)
+ aa[(int)all[i].toChar() - 65] = all[i];
+ }
+
+ protected GappedSequence toSequence
+ (String seq, String description, ParserExceptionHandler eh)
+ {
+ Element[] elements = new Element[seq.length()];
+
+ // cycle through sequence string and generate an set of
+ // amino-acids/gaps.
+ for (int i = 0; i < seq.length(); i++) {
+ if (seq.charAt(i) == Gap.GAP.toChar())
+ elements[i] = Gap.GAP;
+ else {
+ try {
+ elements[i] = aa[((int)seq.charAt(i) - 65)];
+ if (elements[i] == null) {
+ eh.handleException(new UnknownElementException
+ ("Element (" + seq.charAt(i) + ") at position " + (i + 1) +
+ " was not recognised", (i+1), seq,
+ new SimpleIdentifier(description)));
+ elements[i] = Gap.GAP;
+ }
+ } catch (ArrayIndexOutOfBoundsException e) {
+ eh.handleException(new UnknownElementException
+ ("Element (" + seq.charAt(i) + ") at position " + (i + 1) +
+ " was not recognised", (i + 1), seq,
+ new SimpleIdentifier(description)));
+ elements[i] = Gap.GAP;
+ }
+ }
+ }
+
+ return Sequences.getElementsAsGappedSequence
+ (elements, ProteinSequenceType.getInstance(),
+ new SimpleIdentifier(description));
+ }
+} // AbstractProteinAlignmentInputParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractProteinAlignmentInputParser.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/10/13 14:33:23 jns
+ * o sorting out a problem with null elements (X) that I had previously
+ * had working, but I then messed it up trying to be smart. I have sorted
+ * by taking out the actualy formation of the sequence, but supplied the
+ * basic elements for creating the sequence.
+ *
+ * Revision 1.4 2000/09/11 13:19:07 lord
+ * Added identifier support
+ *
+ * Revision 1.3 2000/08/01 14:58:15 jns
+ * o removal of BioObject
+ *
+ * Revision 1.2 2000/07/27 22:34:00 jns
+ * o uncalculated compile problem now sorted - but not sure it is an ideal
+ * solution.
+ *
+ * Revision 1.1 2000/07/27 22:11:33 jns
+ * o mv because now will have output parsers as well as input stuff
+ * o also catered for sequence causeing exceptions - enable tighter exception
+ * handling
+ *
+ * Revision 1.5 2000/07/18 11:10:23 lord
+ * Import rationalisation.
+ * Changes due to removal of biointerface
+ *
+ * Revision 1.4 2000/06/16 11:36:29 jns
+ * o adding chomp of leading gaps into code
+ *
+ * Revision 1.3 2000/06/08 21:22:20 jns
+ * o forgot to remove method parse
+ *
+ * Revision 1.2 2000/06/08 21:18:01 jns
+ * o made the toSequence method, protected rather than public
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.java b/src/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.java
new file mode 100644
index 0000000..60e9cb9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/parsers/AbstractProteinSequenceInputParser.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.parsers; // Package name inserted by JPack
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.SequenceInputParser;
+import uk.ac.man.bioinf.io.UnknownElementException;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * AbstractProteinSequenceInputParser.java
+ *
+ * Provides a root class for all protein sequence parsers.
+ *
+ * Created: Wed Feb 7 15:08:25 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractProteinSequenceInputParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractProteinSequenceInputParser implements SequenceInputParser
+{
+ private static AminoAcid[] aa;
+
+ static
+ {
+ AminoAcid[] all = AminoAcid.getAll();
+ aa = new AminoAcid[26];
+
+ for (int i = 0; i < all.length; i++)
+ aa[(int)all[i].toChar() - 65] = all[i];
+ }
+
+
+ protected Sequence toSequence
+ ( Identifier ident, String seq, ParserExceptionHandler eh )
+ {
+ return Sequences.getElementsAsSequence
+ ( toElements( seq, eh ), ProteinSequenceType.getInstance(), ident );
+ }
+
+ protected Element[] toElements
+ ( String seq, ParserExceptionHandler eh )
+ {
+ Element[] elements = new Element[ seq.length() ];
+
+ for( int i = 0; i < seq.length(); i++ ){
+ int elem = (int)seq.charAt( i ) - 65;
+ if( elem >= elements.length ){
+ eh.handleException( createException( i, (char)elem ) );
+ }
+
+ elements[ i ] = aa[ (int)seq.charAt( i ) - 65 ];
+ if( elements[ i ] == null ){
+ System.out.println( "Element not recognised is " + (seq.charAt( i )) );
+
+ eh.handleException( createException( i, (char)elem ) );
+ }
+ }
+
+ return elements;
+ }
+
+ protected UnknownElementException createException( int position, char elem )
+ {
+ return new UnknownElementException
+ ( "Element (" + elem + ") at position " + (position + 1) +
+ " was not recognised", (position + 1) );
+ }
+
+} // AbstractProteinSequenceInputParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractProteinSequenceInputParser.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:45:48 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.java b/src/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.java
new file mode 100644
index 0000000..208896e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/parsers/FastaSequenceParser.java
@@ -0,0 +1,118 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.parsers; // Package name inserted by JPack
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.SequenceInputParser;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.SimpleIdentifier;
+
+
+/**
+ * FastaSequenceParser.java
+ *
+ *
+ * Created: Wed Feb 7 15:07:45 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: FastaSequenceParser.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class FastaSequenceParser extends AbstractProteinSequenceInputParser
+{
+
+ public Sequence parse( Reader reader, ParserExceptionHandler exh ) throws IOException
+ {
+ String currentLine;
+ BufferedReader read = new BufferedReader( reader );
+
+ while( (currentLine = read.readLine()) != null
+ && !currentLine.startsWith( ">" ) );
+
+ // need to have a specific Identifier for Fasta which is more descriptive.
+ return parseSequence( new SimpleIdentifier( currentLine ), read, exh );
+ }
+
+ public Sequence parse( Identifier ident, Reader reader, ParserExceptionHandler exh )
+ throws IOException
+ {
+ String currentLine;
+ BufferedReader read = new BufferedReader( reader );
+
+ while( !(currentLine = read.readLine() ).startsWith( ">" ) );
+
+ return parseSequence( ident, read, exh );
+ }
+
+ private Sequence parseSequence( Identifier ident, BufferedReader reader, ParserExceptionHandler eh )
+ throws IOException
+ {
+ boolean cont = true;
+ StringBuffer seq = new StringBuffer();
+
+ String currentLine;
+
+ while( (currentLine = reader.readLine()) != null ){
+
+ currentLine = currentLine.trim();
+
+ if( currentLine.endsWith( "*" ) ){
+ cont = false;
+ // lop off the last character, which is the *
+ currentLine = currentLine.substring( 0, currentLine.length() - 2 );
+ }
+
+ seq.append( currentLine );
+ }
+
+ return toSequence( ident, seq.toString(), eh );
+ }
+
+ public String getDescription()
+ {
+ return "Fasta format parser";
+ }
+} // FastaSequenceParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: FastaSequenceParser.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:45:48 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/parsers/MotProteinParser.java b/src/uk/ac/man/bioinf/io/parsers/MotProteinParser.java
new file mode 100644
index 0000000..eb3c220
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/parsers/MotProteinParser.java
@@ -0,0 +1,122 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.parsers; // Package name inserted by JPack
+import java.io.Writer;
+import java.text.DateFormat;
+import java.util.Date;
+import uk.ac.man.bioinf.io.AlignmentOutputParser;
+import uk.ac.man.bioinf.io.InvalidSequenceTypeParserException;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.sequence.InvalidSequenceTypeException;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+import java.io.IOException;
+import uk.ac.man.bioinf.io.SequenceWriterException;
+
+
+/**
+ * MotProteinParser.java
+ *
+ * Mot files are used by several of the applications that are used to
+ * produce PRINTS. Its a very simple format. One line per sequence
+ * (motif files tend to be fairly short alignments). Comments are
+ * designated with a #. PRINTS motif's can't contain gaps so by
+ * definition here this parser does not like gaps and will not write
+ * them out.
+ *
+ * Created: Mon Jan 22 16:44:15 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: MotProteinParser.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class MotProteinParser implements AlignmentOutputParser
+{
+
+ public Writer write( SequenceAlignment sa, Writer writer, ParserExceptionHandler eh )
+ {
+ try{
+
+ // is this off the right type.
+ if( sa.getSequenceType() != ProteinSequenceType.getInstance() ){
+ throw new InvalidSequenceTypeParserException( ProteinSequenceType.getInstance() );
+ }
+
+ writer.write
+ ( "# Produced by Cinema " + DateFormat.getTimeInstance().format( new Date() ) + "\n");
+
+ Sequences.printAlignment( sa );
+
+ for( int i = 1; i < sa.getNumberSequences() + 1; i++ ){
+
+ GappedSequence seq = sa.getSequenceAt( i );
+ Sequences.printSequence( seq );
+
+ if( sa.getInset( i ) != 0 )
+ throw new InvalidSequenceTypeException( "Mot files can not contain any gaps" );
+
+ String seqString = Sequences.getGappedSequenceAsString( seq );
+ writer.write( seqString );
+ writer.write( "\n" );
+ }
+ }
+ catch( InvalidSequenceTypeParserException istpe ){
+ eh.handleException( istpe );
+ }
+ catch( IOException exp ){
+ exp.printStackTrace();
+ eh.handleException( new SequenceWriterException() );
+ }
+ return writer;
+ }
+
+ public String getDescription()
+ {
+ return "Parser for .mot file format." ;
+ }
+} // MotProteinParser
+
+
+
+
+/*
+ * ChangeLog
+ * $Log: MotProteinParser.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/31 18:02:52 lord
+ * Now returns the writer, rather than void. Largely because it can.
+ *
+ * Revision 1.1 2001/01/23 18:00:08 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.java b/src/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.java
new file mode 100644
index 0000000..429b1eb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/parsers/PIRProteinAlignmentParser.java
@@ -0,0 +1,299 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.parsers; // Package name inserted by JPack
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
+import uk.ac.man.bioinf.debug.Debug;
+import uk.ac.man.bioinf.io.AlignmentOutputParser;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.SequenceWriterException;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+import uk.ac.man.bioinf.util.IntArrayList;
+import uk.ac.man.bioinf.io.InvalidSequenceTypeParserException;
+
+
+/**
+ * A filter that reads an alignment in PIR/NBRF protein sequence
+ * format and returns a sequence alignment object. This parser has no
+ * state attached to it, and may be re-entered (ie it is thread safe).
+ *
+ *
+ * Created: Fri May 26 10:18:02 2000
+ *
+ * @author J Selley
+ * @version $Id: PIRProteinAlignmentParser.java,v 1.15 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class PIRProteinAlignmentParser
+ extends AbstractProteinAlignmentInputParser
+ implements AlignmentOutputParser
+{
+
+ /**
+ * This function parses an input reader which contains a (set of)
+ * PIR/NBRF sequence(s), and returns an alignment containing
+ * them. It only reads the protein version of PIR/NBRF format. Any
+ * exceptions thrown up (except the IOException) are packaged up and
+ * sent to an exception handler.
+ *
+ * @param r the input reader
+ * @param eh the exception handler
+ * @return the sequence alignment
+ * @exception IOException if there is an error in the reader
+ */
+ public SequenceAlignment parse(Reader r, ParserExceptionHandler eh)
+ throws IOException
+ {
+ return parse( new NoIdentifier(), r, eh );
+ }
+
+
+ public SequenceAlignment parse( Identifier ident, Reader r, ParserExceptionHandler eh )
+ throws IOException
+ {
+ List seqObjs = new ArrayList();
+ IntArrayList offsets = new IntArrayList();
+ GappedSequence[] sequences;
+ String currentLine, resourceString = "";
+ String seq = "";
+ BufferedReader reader = new BufferedReader(r);
+
+ while ((currentLine = reader.readLine()) != null) {
+ // remove whitespace
+ StringTokenizer st = new StringTokenizer(currentLine);
+ String newCurrentLine = "";
+ while (st.hasMoreTokens()){
+ newCurrentLine += st.nextToken();
+ }
+
+ currentLine = newCurrentLine;
+
+ if (currentLine.startsWith(">P1;")) {
+ // reset the sequence string
+ seq = "";
+
+ // initiate the resource string
+ resourceString = currentLine.substring(4);
+
+ // get the comment line
+ currentLine = reader.readLine();
+ // add comment line to resource string
+ if (currentLine != "")
+ resourceString += " [" + currentLine + "]";
+
+ continue;
+ } else if (currentLine.endsWith("*")) {
+ // remove the asterisk and add the rest of sequence to seq
+ seq += currentLine.substring(0, (currentLine.length() - 1));
+
+ // store the sequence if it isn't empty
+ if (seq != "") {
+ // remove leading gaps
+ GappedSequence s = toSequence(seq, resourceString, eh);
+ try {
+ offsets.add(Sequences.chompLeadingGaps(s));
+ } catch (SequenceVetoException sve) {
+ /* it should be impossible to get a veto here as we have just
+ * created the GappedSequence and have no added any listeners
+ * to it!
+ */
+ if(Debug.debug)
+ Debug.both(this,
+ "ASSERT: veto where there should not be one!",
+ sve);
+ }
+ /* if there is a sequence string, convert it to a gapped
+ * sequence and add it to what will become the alignment.
+ */
+ seqObjs.add(s);
+ }
+ } else {
+ seq += currentLine;
+ }
+ }
+
+ sequences = new GappedSequence[seqObjs.size()];
+ System.arraycopy(seqObjs.toArray(), 0, sequences, 0, sequences.length);
+
+ return new DefaultSequenceAlignment(sequences,
+ ProteinSequenceType.getInstance(),
+ offsets.toArray(), ident );
+ }
+
+ /**
+ * This method parses a sequence alignment and writes it out to the
+ * supplied writer. It formats the output to 80 characters wide.
+ * <p>
+ * <b>N.B.</b>, this method does nothing with the writer other than
+ * write output to it - <i>i.e.</i> it does not close the writer.
+ *
+ * @param sa the sequence alignment to be written.
+ * @param writer the writer to which the sequence is to be written
+ * @param eh the exception handler to which exceptions are parsed.
+ */
+ public Writer write(SequenceAlignment sa, Writer writer,
+ ParserExceptionHandler eh)
+ {
+ /* check that the sequence alignment is a protein sequence
+ * alignment - throw an exception if it isn't
+ */
+ if (sa.getSequenceType() != ProteinSequenceType.getInstance())
+ eh.handleException(new InvalidSequenceTypeParserException
+ (ProteinSequenceType.getInstance()));
+
+
+ // cycle through each sequence in the alignment...
+ for (int i = 0; i < sa.getNumberSequences(); i++) {
+ GappedSequence seq = sa.getSequenceAt(i + 1); // the sequence of interest
+
+ // convert the sequence to a string remembering the inset
+ String inset = "";
+ for (int j = 0; j < sa.getInset(i + 1); j++)
+ inset += "" + Gap.GAP.toChar() + "";
+ String seqString = inset + Sequences.getGappedSequenceAsString(seq);
+ // get the description and source of the sequence if exists
+ String description = seq.getIdentifier().getTitle();
+ String source = seq.getIdentifier().getSource().getTitle();
+ // set the description and source if not already set
+ if (description == "")
+ description = "Unknown protein";
+ if ((source == "") || (source == "No Title"))
+ source = "Unknown source";
+
+ // write the sequence
+ try {
+ // print the header info for the sequence
+ writer.write(">P1;" + description + "\n");
+ writer.write("From: " + source + "\n");
+
+ // print the sequence
+ for( int j = 0; j < seqString.length(); j++ ){
+ writer.write( seqString.charAt( j ) );
+ // 80 chars per line
+ if( ((j + 1) % 80) == 0 ){
+ writer.write( "\n" );
+ }
+ }
+ // write a star to complete the format
+ writer.write("*\n");
+ } catch (IOException e) {
+ eh.handleException(new SequenceWriterException());
+ if (Debug.debug)
+ Debug.both(this, "PIR Parser (writing): IOException caught when " +
+ "writing the sequence " + seq + " " +
+ description + "!", e);
+ }
+ }
+ return writer;
+ }
+
+ /**
+ * Returns that this is a PIR/NBRF protein sequence parser.
+ *
+ * @return the description of this parser
+ */
+ public String getDescription()
+ {
+ return "PIR/NBRF protein sequence parser";
+ }
+} // PIRProteinAlignmentParser
+
+
+
+/*
+ * ChangeLog
+ * $Log: PIRProteinAlignmentParser.java,v $
+ * Revision 1.15 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.14 2001/01/31 18:02:52 lord
+ * Now returns the writer, rather than void. Largely because it can.
+ *
+ * Revision 1.13 2001/01/26 17:12:40 lord
+ * Re-written parser. Fixed two bugs. Now prints 80 char lines (rather
+ * than 79) and no longer mixes off the last line.
+ *
+ * Revision 1.12 2001/01/23 17:59:57 lord
+ * Changed exception handling
+ *
+ * Revision 1.11 2000/12/18 12:13:53 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.10 2000/11/02 17:38:53 jns
+ * o dealing with a pending: moved the code to create the sequence to the
+ * location that was more logical - i.e., when you have got to the end of
+ * each sequence, which in PIR is easy because it is denoted by an '*'.
+ *
+ * Revision 1.9 2000/09/11 13:19:07 lord
+ * Added identifier support
+ *
+ * Revision 1.8 2000/08/21 17:28:41 jns
+ * o addition of output stuff (e.g., write procedure)
+ *
+ * Revision 1.7 2000/07/27 22:13:06 jns
+ * o set to extend Abs. Input parser - name change - will later extend output
+ * parser as well.
+ *
+ * Revision 1.6 2000/07/18 11:10:33 lord
+ * Import rationalisation.
+ * Changes due to removal of biointerface
+ *
+ * Revision 1.5 2000/06/30 09:34:43 jns
+ * o have added setting of sequence offsets and chomping of trailing gaps
+ *
+ * Revision 1.4 2000/06/16 11:36:29 jns
+ * o adding chomp of leading gaps into code
+ *
+ * Revision 1.3 2000/06/16 09:38:52 jns
+ * o added getDescription method to tie with the alteration to the
+ * AlignmentParser interface
+ *
+ * Revision 1.2 2000/06/08 21:21:39 jns
+ * o changed so no longer has state
+ * o tie in with interface
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/test/AlignmentParserIOTest.java b/src/uk/ac/man/bioinf/io/test/AlignmentParserIOTest.java
new file mode 100644
index 0000000..9ea0a61
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/test/AlignmentParserIOTest.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.test; // Package name inserted by JPack
+
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import uk.ac.man.bioinf.io.AlignmentInputParser;
+import uk.ac.man.bioinf.io.AlignmentOutputParser;
+import uk.ac.man.bioinf.io.DefaultParserExceptionHandler;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * AlignmentParserIOTest.java
+ *
+ *
+ * Created: Mon Aug 14 16:46:12 2000
+ *
+ * @author Julian Selley
+ * @version $Id: AlignmentParserIOTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentParserIOTest
+{
+ public static void main(String[] args)
+ {
+ if (args.length != 2) {
+ System.err.println("Usage: java AlignmentParserIOTest <input file> <output file>");
+ System.err.println(" where:");
+ System.err.println(" <input file> : is the sequence filename in PIR format");
+ System.err.println(" <output file> : is the sequence filename for output of the PIR format sequence(s)");
+ System.err.println(" [well I never said it would be a useful test]");
+ System.exit(255);
+ }
+
+ ParserExceptionHandler eh = new DefaultParserExceptionHandler(); // a default exception handler to chuck out any exceptions
+ AlignmentInputParser iParser = new PIRProteinAlignmentParser(); // an input PIR protein alignment parser
+ AlignmentOutputParser oParser = new PIRProteinAlignmentParser(); // an output PIR protein alignment parser
+ FileReader fr; // the file reader to obtain the input alignment
+ Writer fw; // the file writer to pass out the alignment
+ SequenceAlignment alignment = null; // the sequence alignment for storage and output
+
+ try {
+ fr = new FileReader(args[0]);
+ alignment = iParser.parse(fr, eh);
+ System.out.println("There are " + alignment.getNumberSequences() +
+ " sequences in that alignment!");
+ } catch (FileNotFoundException e) {
+ System.err.println("Ooopppss, that file doesn't exist!");
+ System.exit(255);
+ } catch (IOException e) {
+ System.err.println("Ooopppss, got an IO Exception!");
+ e.printStackTrace();
+ System.exit(255);
+ }
+
+ if (alignment.getNumberSequences() > 0) {
+ try {
+ fw = new FileWriter(args[1]);
+ oParser.write(alignment, fw, eh);
+ fw.close();
+ } catch (IOException e) {
+ System.err.println("Ooopppss, got an IO Exception on output!");
+ e.printStackTrace();
+ System.exit(255);
+ }
+ } else {
+ System.err.println("The sequence alignment has no sequences in it!");
+ System.exit(255);
+ }
+ }
+} // AlignmentParserIOTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentParserIOTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/08/21 17:21:23 jns
+ * o added output parser stuff to package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/io/test/AlignmentParserInputTest.java b/src/uk/ac/man/bioinf/io/test/AlignmentParserInputTest.java
new file mode 100644
index 0000000..04af244
--- /dev/null
+++ b/src/uk/ac/man/bioinf/io/test/AlignmentParserInputTest.java
@@ -0,0 +1,101 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.io.test; // Package name inserted by JPack
+
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import uk.ac.man.bioinf.io.AlignmentInputParser;
+import uk.ac.man.bioinf.io.DefaultParserExceptionHandler;
+import uk.ac.man.bioinf.io.ParserExceptionHandler;
+import uk.ac.man.bioinf.io.parsers.PIRProteinAlignmentParser;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * AlignmentParserInputTest.java
+ *
+ *
+ * Created: Wed Jun 7 19:18:07 2000
+ *
+ * @author J Selley
+ * @version $Id: AlignmentParserInputTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentParserInputTest
+{
+ public static void main(String[] args)
+ {
+ if (args.length == 0) {
+ System.err.println("No filename supplied!");
+ System.exit(255);
+ }
+
+ ParserExceptionHandler eh = new DefaultParserExceptionHandler();
+ AlignmentInputParser parser = new PIRProteinAlignmentParser();
+ FileReader fr;
+ SequenceAlignment alignment;
+
+ try {
+ fr = new FileReader(args[0]);
+ alignment = parser.parse(fr, eh);
+ System.out.println("There are " + alignment.getNumberSequences() + " sequences in that alignment!");
+ System.out.println(" they were:");
+ Sequences.printAlignment(alignment);
+ } catch (FileNotFoundException e) {
+ System.err.println("Ooopppss, that file doesn't exist!");
+ System.exit(255);
+ } catch (IOException e) {
+ System.err.println("Ooopppss, got an IO Exception!");
+ e.printStackTrace();
+ System.exit(255);
+ }
+ }
+} // AlignmentParserInputTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentParserInputTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/27 22:35:08 jns
+ * o mv from AlignmentParserTest to AlignmentParserInputTest as this allows
+ * for output stuff to be done now.
+ *
+ * Revision 1.2 2000/06/08 21:23:30 jns
+ * o changed to fit new non-state parser model
+ *
+ * Revision 1.1 2000/06/08 12:32:17 jns
+ * o I/O stuff written to parse in a sequence file
+ * o currently only written the PIRProtein parser
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.java b/src/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.java
new file mode 100644
index 0000000..8be6332
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/AbstractEnumeratedModuleIdentifier.java
@@ -0,0 +1,158 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+import uk.ac.man.bioinf.util.AbstractEnumeration;
+import java.lang.reflect.Field;
+import uk.ac.man.bioinf.debug.Debug;
+import java.lang.reflect.Modifier;
+
+
+/**
+ * AbstractEnumeratedModuleIdentifier.java
+ *
+ *
+ * Created: Sun May 7 17:42:13 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractEnumeratedModuleIdentifier.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractEnumeratedModuleIdentifier extends AbstractEnumeration
+ implements ModuleIdentifier
+{
+ private String moduleName, className;
+ private boolean isInterface;
+
+ public AbstractEnumeratedModuleIdentifier( String className, String toString )
+ {
+ this( className, toString, false );
+ }
+
+ public AbstractEnumeratedModuleIdentifier( String className, String toString, boolean isInterface )
+ {
+ super( toString );
+ this.className = className;
+ this.isInterface = isInterface;
+ }
+
+ public static ModuleIdentifier[] getAllIdentifiers( Class cla )
+ {
+ // java casting,
+ // I hate java casting,
+ // tra-la, tra-la, la la ley
+ AbstractEnumeration[] enumArray = getAllElements( cla );
+ ModuleIdentifier[] moduleArray = new ModuleIdentifier[ enumArray.length ];
+
+ System.arraycopy( enumArray, 0, moduleArray, 0, enumArray.length );
+ return moduleArray;
+ }
+
+ /**
+ * This method uses reflection to make sure that the module name
+ * returned is the same as its Field. This means that I dont have to
+ * ensure that I get problems with name typo.
+ */
+ private void initModuleNames()
+ {
+ Class cla = getClass();
+ Field[] fields = cla.getDeclaredFields();
+ for( int i = 0; i < fields.length; i++ ){
+ try{
+ // only bother for static fields. We need to check this
+ // otherwise the get( null ) call with raise a NPE also
+ if( Modifier.isStatic( fields[ i ].getModifiers() ) ){
+ if( fields[ i ].get( null ) == this ){
+ moduleName = fields[ i ].getName();
+ }
+ }
+ }
+ catch( IllegalAccessException iae ){
+ // This can not happen because the class is this class, and so
+ // we can access everything
+ if( Debug.debug )
+ Debug.both( this, "Design mistake in software!", iae );
+ }
+ }
+ }
+
+ public String getModuleName()
+ {
+ if( moduleName == null )
+ initModuleNames();
+ return moduleName;
+ }
+
+ public String getClassName()
+ {
+ return className;
+ }
+
+ public boolean isInterface()
+ {
+ return isInterface;
+ }
+
+ public String toString()
+ {
+ return "Enumerated Module Identifier:- " + super.toString();
+ }
+} // AbstractEnumeratedModuleIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractEnumeratedModuleIdentifier.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.2 2000/08/03 16:40:37 lord
+ * Got Interface Modules working correctly which required quite a few changes
+ *
+ * Revision 1.1 2000/07/25 12:00:36 lord
+ * Renamed from AbstractEnumeratedModuleIndentifier
+ *
+ * Revision 1.4 2000/06/27 16:07:36 lord
+ * Removed debug System.out
+ *
+ * Revision 1.3 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.2 2000/05/30 16:23:35 lord
+ * Method name changes
+ *
+ * Revision 1.1 2000/05/08 18:06:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/DefaultModuleContext.java b/src/uk/ac/man/bioinf/module/DefaultModuleContext.java
new file mode 100644
index 0000000..3998349
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/DefaultModuleContext.java
@@ -0,0 +1,74 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+/**
+ * DefaultModuleContext.java
+ *
+ *
+ * Created: Tue May 23 15:03:25 2000
+ *
+ * @author J Selley
+ * @version $Id: DefaultModuleContext.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultModuleContext extends ModuleContext
+{
+ private ModuleIdentifier identifier;
+ private ModuleStorageStructure store;
+
+ public DefaultModuleContext(ModuleIdentifier identifier, ModuleStorageStructure struct)
+ {
+ this.identifier = identifier;
+ this.store = struct;
+ }
+
+ public ModuleIdentifier getIdentifier()
+ {
+ return this.identifier;
+ }
+
+ public Object getConfig()
+ {
+ return this.store.getConfig();
+ }
+} // DefaultModuleContext
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultModuleContext.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/24 13:08:32 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.java b/src/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.java
new file mode 100644
index 0000000..26daeb0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/DefaultModuleFactoryInstance.java
@@ -0,0 +1,317 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+import java.util.HashMap;
+import java.util.Iterator;
+import uk.ac.man.bioinf.debug.Debug;
+
+
+/**
+ * DefaultModuleFactoryInstance.java
+ *
+ *
+ * Created: Thu May 11 13:02:22 2000
+ *
+ * @author J Selley
+ * @version $Id: DefaultModuleFactoryInstance.java,v 1.13 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultModuleFactoryInstance
+ implements ModuleFactoryInstance
+{
+ private HashMap mods = new HashMap();
+ private HashMap classnames = new HashMap();
+ private HashMap moduleNames = new HashMap();
+
+ public DefaultModuleFactoryInstance() {}
+
+ public Module load(ModuleIdentifier identifier) throws ModuleException
+ {
+ Module module;
+
+ // make sure that we have the concrete version of this identifier
+ identifier = getConcreteIdentifier( identifier );
+
+
+ // if the identifier has not been loaded previously
+ if ( ( module = ((ModuleStorageStructure)mods.get(identifier)).getModule() ) == null ) {
+
+ // try and create the module
+ try {
+ Class modClass = Class.forName(identifier.getClassName());
+ module = (Module)modClass.newInstance();
+
+
+ ModuleStorageStructure struct = (ModuleStorageStructure)mods.get(identifier);
+ // set the context
+ module.setContext( struct.getContext() );
+
+ // run the load procedure on this module
+ module.load();
+
+ // store module if it has been generated
+ struct.setModule(module);
+
+ // get all required identifiers
+ ModuleIdentifier[] reqIdents = module.getRequiredIdentifiers().toArray();
+ // check if they have been created previously...
+ Module[] requiredModules = new Module[ reqIdents.length ];
+
+ for (int i = 0; i < reqIdents.length; i++) {
+ if (!(mods.containsKey(reqIdents[i]))) {
+ // add the identifier
+ addIdentifier(reqIdents[i]);
+ }
+ // load the required module
+ requiredModules[ i ] = load(reqIdents[i]);
+ }
+ struct.addRequiredModules( requiredModules );
+ }
+ catch( NullPointerException npe ){
+ npe.printStackTrace();
+
+ throw new ModuleException( identifier.getClassName(), ModuleExceptionType.MODULE_CLASS_NOT_FOUND );
+ }
+ catch (ClassNotFoundException e) {
+ throw new ModuleException( identifier.getClassName(), ModuleExceptionType.MODULE_CLASS_NOT_FOUND);
+ }
+ catch (InstantiationException e) {
+ throw new ModuleException( identifier.getClassName(), ModuleExceptionType.MODULE_INIT_PROBLEM);
+ }
+ catch (IllegalAccessException e) {
+ throw new ModuleException( identifier.getClassName(), ModuleExceptionType.MODULE_INIT_PROBLEM);
+ }
+ }
+ return module;
+ }
+
+ private ModuleIdentifier getConcreteIdentifier( ModuleIdentifier ident )
+ {
+ if( ident.isInterface() ){
+ ModuleStorageStructure value = (ModuleStorageStructure)
+ this.mods.get( ident );
+
+ return value.getConcreteIdentifier();
+ }
+ else{
+ return ident;
+ }
+ }
+
+ public void addIdentifier(ModuleIdentifier identifier)
+ {
+ if( mods.get( identifier ) == null ){
+
+ // generate module storage structure
+ ModuleStorageStructure struct = new ModuleStorageStructure();
+ // and set the module context
+ ModuleContext context = new DefaultModuleContext(identifier, struct);
+ context.setModuleFactory( this );
+ struct.setContext( context );
+
+ // store identifier and storage structure
+ this.mods.put(identifier, struct);
+ // store class and module names in easy hash look up
+ this.classnames.put(identifier.getClassName(), identifier);
+ moduleNames.put( identifier.getModuleName(), identifier );
+ }
+ }
+
+ public void addIdentifier(ModuleIdentifier[] identifiers)
+ {
+ for (int i = 0; i < identifiers.length; i++) {
+ addIdentifier(identifiers[i]);
+ }
+ }
+
+ public ModuleIdentifier resolveModuleName( String moduleName )
+ {
+ return (ModuleIdentifier)moduleNames.get( moduleName );
+ }
+
+ public ModuleIdentifier resolveClassName(String classname)
+ {
+ return (ModuleIdentifier)this.classnames.get(classname);
+ }
+
+ public void setModule(ModuleIdentifier identifier, Module module)
+ throws ModuleException
+ {
+ ModuleStorageStructure value = (ModuleStorageStructure)
+ this.mods.get(identifier);
+ value.setModule(module);
+ }
+
+ public Module getModule(ModuleIdentifier identifier) throws ModuleException
+ {
+ //ensure that we have the concrete version of this identifier
+ identifier = getConcreteIdentifier( identifier );
+
+ Module mod = ((ModuleStorageStructure)this.mods.get(identifier)).
+ getModule();
+
+ if( mod == null ){
+ throw new ModuleException( "Attempt to start a module " + identifier.getModuleName() + " when it does not exist",
+ ModuleExceptionType.MODULE_DOES_NOT_EXIST );
+ }
+
+ // start the module if it isn't already started
+ if (!mod.isStarted()) {
+ if (Debug.debug)
+ Debug.message(this, "Module Factory: starting module " + identifier.getModuleName());
+ mod.runStart();
+ }
+ return mod;
+ }
+
+ public void addRequiredModules(ModuleIdentifier identifier, Module[] reqMods)
+ {
+ ModuleStorageStructure value = (ModuleStorageStructure)
+ this.mods.get(identifier);
+ value.addRequiredModules(reqMods);
+ }
+
+ public void addRequiredModule(ModuleIdentifier identifier, Module reqMod)
+ {
+ ModuleStorageStructure value = (ModuleStorageStructure)
+ this.mods.get(identifier);
+ value.addRequiredModule(reqMod);
+ }
+
+ public ModuleList getRequiredModules(ModuleIdentifier identifier)
+ {
+ return ((ModuleStorageStructure)this.mods.get(identifier)).
+ getRequiredModules();
+ }
+
+ public void setConfig(ModuleIdentifier identifier, Object config)
+ {
+ ModuleStorageStructure value = (ModuleStorageStructure)
+ this.mods.get(identifier);
+ value.setConfig(config);
+ }
+
+ public Object getConfig(ModuleIdentifier identifier)
+ {
+ return ((ModuleStorageStructure)this.mods.get(identifier)).
+ getConfig();
+ }
+
+ public void setConcreteIdentifier( ModuleIdentifier abstractIdentifier, ModuleIdentifier concreteIdentifier )
+ {
+ ModuleStorageStructure value = (ModuleStorageStructure)
+ this.mods.get( abstractIdentifier );
+ value.setConcreteIdentifier( concreteIdentifier );
+ }
+
+ public boolean isModuleAvailable(ModuleIdentifier identifier)
+ {
+ //ensure that we have the concrete version of this identifier
+ identifier = getConcreteIdentifier( identifier );
+
+ Module mod = ((ModuleStorageStructure)this.mods.get(identifier)).
+ getModule();
+
+ return (mod != null);
+ }
+
+ public void destroy()
+ {
+ Iterator iter = mods.values().iterator();
+ while( iter.hasNext() ){
+ Module mod = ((ModuleStorageStructure)iter.next()).getModule();
+ if( mod != null ) mod.destroy();
+ }
+
+ // (PENDING:- PL) Need to put in checks for null pointer errors
+ // and throw module "attempt to use destroyed factory" errors.
+ mods = null;
+ classnames = null;
+ moduleNames = null;
+ }
+} // DefaultModuleFactoryInstance
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultModuleFactoryInstance.java,v $
+ * Revision 1.13 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.12 2001/02/20 14:48:17 lord
+ * removed typo
+ *
+ * Revision 1.11 2001/02/19 17:50:52 lord
+ * Removed debug statements
+ *
+ * Revision 1.10 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.9 2001/01/26 17:13:24 lord
+ * Improved exception handling
+ *
+ * Revision 1.8 2000/09/15 16:31:23 lord
+ * Modifications to remove the ModuleFactory static class. This turned
+ * out to be rather limiting and also entirely unnecessary so I removed
+ * it.
+ *
+ * Revision 1.7 2000/08/03 16:40:37 lord
+ * Got Interface Modules working correctly which required quite a few changes
+ *
+ * Revision 1.6 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.5 2000/05/30 16:24:41 lord
+ * resolveModuleName added.
+ * Small changes to exception handling
+ *
+ * Revision 1.4 2000/05/24 20:25:00 jns
+ * o load() - check that the module hasn't been loaded already
+ * o addIdentifier(MI[] ) added to smooth later code writing
+ * o getModule(MI ) starts the module if not already started, before returning it
+ * o put in a resolveClassName method so that by having a class name you can obtain
+ * the module identifier
+ *
+ * Revision 1.3 2000/05/24 19:19:00 lord
+ * Added context object.
+ * Provided Modules sorted
+ *
+ * Revision 1.2 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ * Revision 1.1 2000/05/24 13:09:42 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/GenericModuleIdentifier.java b/src/uk/ac/man/bioinf/module/GenericModuleIdentifier.java
new file mode 100644
index 0000000..4190bd0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/GenericModuleIdentifier.java
@@ -0,0 +1,96 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+/**
+ * GenericModuleIdentifier.java
+ *
+ *
+ * Created: Mon May 15 16:02:45 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GenericModuleIdentifier.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class GenericModuleIdentifier implements ModuleIdentifier
+{
+
+ private String className, moduleName;
+ private boolean isInterface;
+
+ public GenericModuleIdentifier( String className, String moduleName, boolean isInterface )
+ {
+ this.className = className;
+ this.moduleName = moduleName;
+ }
+
+ public boolean isInterface()
+ {
+ return isInterface;
+ }
+
+ public String getClassName()
+ {
+ return className;
+ }
+
+ public String getModuleName()
+ {
+ return moduleName;
+ }
+} // GenericModuleIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: GenericModuleIdentifier.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.4 2000/08/01 17:14:28 lord
+ * Now have different Identifier for non concrete instances
+ *
+ * Revision 1.3 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.2 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ * Revision 1.1 2000/05/15 16:24:15 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/Module.java b/src/uk/ac/man/bioinf/module/Module.java
new file mode 100644
index 0000000..a6df530
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/Module.java
@@ -0,0 +1,298 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayList;
+import uk.ac.man.bioinf.debug.Debug;
+
+
+/**
+ * Module.java
+ *
+ * Represents a module, the main constituent of a modular
+ * architectured program. It is associated with the module identifier
+ * and context classes.
+ *
+ * Created: Wed Apr 19 14:17:05 2000
+ *
+ * @author J Selley
+ * @version $Id: Module.java,v 1.10 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class Module
+{
+ /**
+ * Returns a module identifier for this module. Simply performs a
+ * delegation to the module context.
+ *
+ * @return this modules identifier
+ */
+ public ModuleIdentifier getIdentifier()
+ {
+ // convenience - delegates function to module context
+ return getContext().getIdentifier();
+ }
+
+ /**
+ * Returns the required modules for this module (ie: the modules
+ * that are necessary in order for this module to function). Simple
+ * delegation to the module context.
+ *
+ * @return the required modules
+ */
+ public ModuleList getRequiredModules()
+ {
+ return getContext().getRequiredModules();
+ }
+
+ public Module getRequiredModule( ModuleIdentifier ident )
+ {
+ ModuleList list = getRequiredModules();
+ int size = list.size();
+ for( int i = 0; i < size; i++ ){
+ if( list.get( i ).getIdentifier() == ident ){
+ return list.get( i );
+ }
+ }
+ throw new NoSuchRequiredModule( ident );
+ }
+
+ /**
+ * Returns the module identifiers for the required modules. This
+ * places a call on getRequiredModules, which is delegated to the
+ * module context. It may require over-riding inorder to improve the
+ * efficiency of the method.
+ *
+ * @return the required module identifiers
+ */
+ public ModuleIdentifierList getRequiredIdentifiers()
+ {
+ return new ModuleIdentifierList( new ArrayList() );
+ }
+
+ /**
+ * Returns the modules context.
+ *
+ * @return the modules context
+ */
+ public final ModuleContext getContext()
+ {
+ return context;
+ }
+
+ private ModuleContext context;
+ public final void setContext( ModuleContext context )
+ {
+ this.context = context;
+ }
+
+ /**
+ * Returns the version of this module.
+ *
+ * @return the version
+ */
+ public abstract String getVersion();
+
+ /**
+ * The method called for the load of this module.
+ *
+ * @exception ModuleLoadException if a loading error occurs
+ */
+ public void load() throws ModuleException {}
+
+ private boolean started = false;
+ /**
+ * The method called externally to initiate the modules function.
+ */
+ public void start()
+ {
+ }
+
+ public void runStart()
+ {
+ if( Debug.debug )
+ Debug.message( this, "Module: Starting module " + getIdentifier() );
+ started = true;
+ start();
+ }
+
+ /**
+ * Returns whether the module has been started (ie: the start method
+ * run).
+ *
+ * @return T/F status of call on start() method
+ */
+ public final boolean isStarted()
+ {
+ return this.started;
+ }
+
+ private boolean destroyed = false;
+ public boolean isDestroyed()
+ {
+ return destroyed;
+ }
+
+ /**
+ * The method called, from an external source, to remove this module
+ * and prepare it for garbage collection.
+ */
+ public void destroy()
+ {
+ if( Debug.debug ){
+ Debug.message( this, "MODULE: Destroying module " + getIdentifier() );
+ }
+
+ context = null;
+ destroyed = true;
+ }
+
+ public void finalize() throws Throwable
+ {
+ //System.out.println( "FINALIZE: " + this );
+ }
+
+ // Property Change Support
+ // do lazy instantiation. I don't really want to increase the over
+ // head of this class
+ private PropertyChangeSupport supp;
+ public synchronized void addPropertyChangeListener( PropertyChangeListener listener )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.addPropertyChangeListener( listener );
+ }
+
+ public synchronized void removePropertyChangeListener( PropertyChangeListener listener )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.removePropertyChangeListener( listener );
+ }
+
+ public synchronized void addPropertyChangeListener( String propertyName, PropertyChangeListener listener )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.addPropertyChangeListener( propertyName, listener );
+ }
+
+ public synchronized void removePropertyChangeListener
+ ( String propertyName, PropertyChangeListener listener)
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.addPropertyChangeListener( propertyName, listener );
+ }
+
+ protected synchronized void firePropertyChange( String propertyName, Object oldValue, Object newValue )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.firePropertyChange( propertyName, oldValue, newValue );
+ }
+
+ protected synchronized void firePropertyChange( String propertyName, int oldValue, int newValue )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.firePropertyChange( propertyName, oldValue, newValue );
+ }
+
+ protected synchronized void firePropertyChange( PropertyChangeEvent event )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ supp.firePropertyChange( event );
+ }
+
+ public synchronized boolean hasListeners( String propertyName )
+ {
+ if( supp == null ){
+ supp = new PropertyChangeSupport( this );
+ }
+ return supp.hasListeners( propertyName );
+ }
+} // Module
+
+
+
+/*
+ * ChangeLog
+ * $Log: Module.java,v $
+ * Revision 1.10 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.9 2000/12/18 12:14:15 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.8 2000/11/13 15:35:58 lord
+ * Now throws a RuntimeException if a required module is not found.
+ * This is better than getting the NPE that invariably resulted
+ * from just returning a null.
+ *
+ * Revision 1.7 2000/09/15 16:31:23 lord
+ * Modifications to remove the ModuleFactory static class. This turned
+ * out to be rather limiting and also entirely unnecessary so I removed
+ * it.
+ *
+ * Revision 1.6 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.5 2000/05/30 16:26:23 lord
+ * runStart() method.
+ *
+ * Revision 1.4 2000/05/24 20:30:49 jns
+ * o created an isStarted() function [final] to check whether the module has been
+ * started.
+ *
+ * Revision 1.3 2000/05/24 19:20:30 lord
+ * getRequiredIdentifiers made concrete
+ * Context methods coded
+ *
+ * Revision 1.2 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ * Revision 1.1 2000/05/24 13:09:42 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/ModuleContext.java b/src/uk/ac/man/bioinf/module/ModuleContext.java
new file mode 100644
index 0000000..cf236f7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleContext.java
@@ -0,0 +1,156 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+
+/**
+ * ModuleContext.java
+ *
+ * Gives context to a module (e.g: configuration information).
+ *
+ * Created: Tue Apr 18 19:17:55 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleContext.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class ModuleContext
+{
+ private ModuleFactoryInstance moduleFactory;
+
+ public void setModuleFactory( ModuleFactoryInstance moduleFactory )
+ {
+ this.moduleFactory = moduleFactory;
+ }
+
+ public ModuleFactoryInstance getModuleFactory()
+ {
+ return moduleFactory;
+ }
+
+ /**
+ * Returns whether a module is available for use, given the
+ * identifier. Allows for optional modules.
+ *
+ * @param identifier the module identifier for the optional module
+ * @return the availability of the module
+ */
+ public boolean isModuleAvailable(ModuleIdentifier identifier)
+ {
+ return moduleFactory.isModuleAvailable(identifier);
+ }
+
+ /**
+ * Returns a module by interfacing with the ModuleHandlerFactory. It
+ * is designed to allow use of optional modules.
+ *
+ * @param identifier the module identifier
+ * @return the module
+ */
+ public Module getModule(ModuleIdentifier identifier) throws ModuleException
+ {
+ return moduleFactory.getModule(identifier);
+ }
+
+ /**
+ * This method resolves a module name into a ModuleIdentifier. Generally
+ * speaking this method is not the preferred mechanisms for getting a
+ * ModuleIdentifier. If a ModuleIdentifier extends
+ * AbstractEnumeratedModuleIdentifier, then they can be directly accessed in a
+ * way which is compile time type safe.
+ * @param moduleName
+ * @return
+ */
+ public ModuleIdentifier resolveModuleName( String moduleName )
+ {
+ return moduleFactory.resolveModuleName( moduleName );
+ }
+
+ /**
+ * Returns the associated module for this context.
+ *
+ * @return the module
+ */
+ public Module getModule() throws ModuleException
+ {
+ return moduleFactory.getModule(getIdentifier());
+ }
+
+ private ModuleList requiredModules;
+
+ public ModuleList getRequiredModules()
+ {
+ if( requiredModules == null ){
+ requiredModules = moduleFactory.getRequiredModules( getIdentifier() );
+ }
+ return requiredModules;
+ }
+
+ /**
+ * Returns the modules identifier.
+ *
+ * @return the module identifier
+ */
+ public abstract ModuleIdentifier getIdentifier();
+
+ /**
+ * Returns an object representing the configuration of the module.
+ *
+ * @return the configuration
+ */
+ public abstract Object getConfig();
+}// ModuleContext
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleContext.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.4 2000/09/15 16:31:23 lord
+ * Modifications to remove the ModuleFactory static class. This turned
+ * out to be rather limiting and also entirely unnecessary so I removed
+ * it.
+ *
+ * Revision 1.3 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.2 2000/05/30 16:26:42 lord
+ * resolveModuleName method
+ *
+ * Revision 1.1 2000/05/24 13:08:32 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/ModuleException.java b/src/uk/ac/man/bioinf/module/ModuleException.java
new file mode 100644
index 0000000..bfd249c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleException.java
@@ -0,0 +1,104 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+/**
+ * ModuleException.java
+ *
+ * An exception thrown if a module does not load sucessfully.
+ *
+ * Created: Tue May 9 18:45:35 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleException.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ModuleException extends Exception
+{
+ private ModuleExceptionType id;
+ private Throwable throwable;
+
+ public ModuleException(String message)
+ {
+ super(message);
+ }
+
+ public ModuleException(ModuleExceptionType id)
+ {
+ super(id.toString());
+ this.id = id;
+ }
+
+ public ModuleException( Throwable throwable )
+ {
+ super( throwable.toString() );
+ this.throwable = throwable;
+ }
+
+ public ModuleException(String message, ModuleExceptionType id)
+ {
+ super(message);
+ this.id = id;
+ }
+
+ public ModuleException( String message, ModuleExceptionType id, Throwable throwable )
+ {
+ this( message, id );
+ this.throwable = throwable;
+ }
+
+ public Throwable getThrowable()
+ {
+ return throwable;
+ }
+
+ public ModuleExceptionType getID()
+ {
+ return this.id;
+ }
+} // ModuleException
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleException.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/13 16:33:02 lord
+ * New constructor
+ *
+ * Revision 1.2 2000/08/03 16:40:37 lord
+ * Got Interface Modules working correctly which required quite a few changes
+ *
+ * Revision 1.1 2000/05/24 13:08:32 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/ModuleExceptionType.java b/src/uk/ac/man/bioinf/module/ModuleExceptionType.java
new file mode 100644
index 0000000..f0d7b3e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleExceptionType.java
@@ -0,0 +1,97 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.util.AbstractEnumeration;
+
+
+/**
+ * This class provides an identifier for the module exception that has
+ * been thrown, rather than string comparisons needing to be carried
+ * out.
+ *
+ *
+ * Created: Mon May 22 11:26:22 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleExceptionType.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public final class ModuleExceptionType extends AbstractEnumeration
+{
+ private ModuleExceptionType(String message)
+ {
+ super(message);
+ }
+
+ public static final ModuleExceptionType MODULE_DOES_NOT_EXIST
+ = new ModuleExceptionType( "Module does not exist ");
+
+ /**
+ * Indicates a failed attempt to resolve a module name
+ */
+ public static final ModuleExceptionType MODULE_RESOLVE_FAIL =
+ new ModuleExceptionType( "Module failed to resolve module name " );
+
+ /**
+ * The module has previously been defined and created.
+ */
+ public static final ModuleExceptionType MODULE_EXISTS =
+ new ModuleExceptionType("Module already defined in storage structure");
+
+ /**
+ * The module class was not found in the location stated.
+ */
+ public static final ModuleExceptionType MODULE_CLASS_NOT_FOUND =
+ new ModuleExceptionType("Module class not found");
+
+ /**
+ * Creating and instantiating the module generated a problem.
+ */
+ public static final ModuleExceptionType MODULE_INIT_PROBLEM =
+ new ModuleExceptionType("Module instantiation caused a problem");
+} // ModuleExceptionType
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleExceptionType.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.2 2001/01/26 17:13:31 lord
+ * New type
+ *
+ * Revision 1.1 2000/05/24 13:08:32 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/ModuleFactoryInstance.java b/src/uk/ac/man/bioinf/module/ModuleFactoryInstance.java
new file mode 100644
index 0000000..890946a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleFactoryInstance.java
@@ -0,0 +1,182 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+
+/**
+ * ModuleFactoryInstance.java
+ *
+ * This interface is designed to provide a means of storing loaded
+ * modules and their associated identifiers. It also allows
+ * configuration of the module.
+ *
+ * This is instance is called from the ModuleFactory which simply
+ * relays the requests here.
+ *
+ * Created: Tue May 9 13:53:20 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleFactoryInstance.java,v 1.10 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ModuleFactoryInstance
+{
+ /**
+ * Returns whether a module is available for use. This allows the
+ * use of optional modules.
+ *
+ * @param identifier the module identifier
+ * @return the availability of the target module
+ */
+ public boolean isModuleAvailable(ModuleIdentifier identifier);
+
+ /**
+ * Returns the module, given the module identifier.
+ *
+ * @param identifier the module identifier
+ * @return the module
+ */
+ public Module getModule(ModuleIdentifier identifier) throws ModuleException;
+
+ /**
+ * Returns the modules required by the given module.
+ *
+ * @param identifier the module identifier of the module of interest
+ * @return the required modules
+ */
+ public ModuleList getRequiredModules(ModuleIdentifier identifier);
+
+ /**
+ * Sets the config to a particular module described by an identifier.
+ *
+ * @param identifier the identifier
+ * @param config the config
+ */
+ public void setConfig(ModuleIdentifier identifier, Object config);
+
+ /**
+ * Returns the config object a given module
+ */
+ public Object getConfig( ModuleIdentifier identifier );
+
+ /**
+ * Set the concrete identifier for a given abstract identifier.
+ */
+ public void setConcreteIdentifier( ModuleIdentifier abstractIdentifer, ModuleIdentifier concreteIdentifier );
+
+ /**
+ * Adds an identifier to the factory storage mechanism.
+ *
+ * @param identifier the identifier
+ */
+ public void addIdentifier(ModuleIdentifier identifier);
+
+ /**
+ * Adds identifiers to the factory storage mechanism.
+ *
+ * @param identifiers an array of identifiers
+ */
+ public void addIdentifier(ModuleIdentifier[] identifiers);
+
+ /**
+ * Resolve a module name into a ModuleIdentifier
+ * @param moduleName the name of the module
+ */
+ public ModuleIdentifier resolveModuleName( String moduleName );
+
+ /**
+ * Resolves a classname of a module into the module identifier.
+ *
+ * @param classname the classname of the module
+ * @return the module identifier
+ */
+ public ModuleIdentifier resolveClassName(String className);
+
+ /**
+ * Loads the module associated with a particular identifier. This
+ * will include a call to the load method of the module. It should
+ * also subsequently check that all requried modules are loaded as
+ * well.
+ *
+ * @param identifier the identifier
+ */
+ public Module load(ModuleIdentifier identifier) throws ModuleException;
+
+ /**
+ * Destroy all of the module instances, and remove all the internal
+ * data structures of this Factory.
+ */
+ public void destroy();
+
+
+}// ModuleFactoryInstance
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleFactoryInstance.java,v $
+ * Revision 1.10 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.9 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.8 2001/01/26 17:13:45 lord
+ * Can now get config as well as set it.
+ *
+ * Revision 1.7 2000/09/15 16:31:23 lord
+ * Modifications to remove the ModuleFactory static class. This turned
+ * out to be rather limiting and also entirely unnecessary so I removed
+ * it.
+ *
+ * Revision 1.6 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.5 2000/05/30 16:27:34 lord
+ * resolveModuleName method
+ * resolveClassName method
+ *
+ * Revision 1.4 2000/05/24 21:21:15 jns
+ * o added addIdentifier(MI[] ) (I think)
+ * o added resolveClassName function
+ *
+ * Revision 1.3 2000/05/24 19:21:03 lord
+ * Changed return type of load method
+ *
+ * Revision 1.2 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ * Revision 1.1 2000/05/24 13:09:42 jns
+ * o initial coding of module package
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/module/ModuleIdentifier.java b/src/uk/ac/man/bioinf/module/ModuleIdentifier.java
new file mode 100644
index 0000000..5f64b35
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleIdentifier.java
@@ -0,0 +1,82 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+
+/**
+ * ModuleIdentifier.java
+ *
+ * A thin tag for a module, rather than banding round modules.
+ *
+ * Created: Wed Apr 26 17:05:48 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleIdentifier.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ModuleIdentifier
+{
+ /**
+ * Returns whether this module is an interface.
+ *
+ * @return whether this module is an interface.
+ */
+ public boolean isInterface();
+
+ /**
+ * Returns the string of the class name.
+ *
+ * @return the class name
+ */
+ public String getClassName();
+
+ /**
+ * Returns the name of the module being defined.
+ *
+ * @return the name
+ */
+ public String getModuleName();
+}// ModuleIdentifier
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.1 2000/05/24 13:08:32 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/ModuleIdentifierList.java b/src/uk/ac/man/bioinf/module/ModuleIdentifierList.java
new file mode 100644
index 0000000..c284063
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleIdentifierList.java
@@ -0,0 +1,180 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+import java.util.List;
+
+
+/**
+ * To provide a list of module identifiers in a type safe manor. This
+ * is basically a thin wrapper to list, specially targeted for
+ * module identifiers.
+ *
+ *
+ * Created: Wed May 24 15:06:49 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleIdentifierList.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ModuleIdentifierList
+{
+ private List list;
+
+ public ModuleIdentifierList(List list)
+ {
+ this.list = list;
+ }
+
+ /**
+ * Adds a module identifier to the list.
+ *
+ * @param m the module identifier
+ * @return the success of the addition
+ */
+ public boolean add(ModuleIdentifier m)
+ {
+ return this.list.add(m);
+ }
+
+ /**
+ * Clear the list.
+ */
+ public void clear()
+ {
+ this.list.clear();
+ }
+
+ /**
+ * Returns whether a module identifier is contained in this list.
+ *
+ * @param m the query module identifier
+ * @return T/F exists
+ */
+ public boolean contains(ModuleIdentifier m)
+ {
+ return this.list.contains(m);
+ }
+
+ /**
+ * Returns the module identifier at a given index.
+ *
+ * @param i the index
+ * @return the module identifier
+ */
+ public ModuleIdentifier get(int i)
+ {
+ return (ModuleIdentifier)this.list.get(i);
+ }
+
+ /**
+ * Returns the index of a module identifier.
+ *
+ * @param m the module identifier
+ * @return the index
+ */
+ public int indexOf(ModuleIdentifier m)
+ {
+ return this.list.indexOf(m);
+ }
+
+ /**
+ * Returns whether the list is empty.
+ *
+ * @return T/F is the list empty
+ */
+ public boolean isEmpty()
+ {
+ return this.list.isEmpty();
+ }
+
+ /**
+ * Removes a module identifier at a specific index.
+ *
+ * @param i the index of the module identifier
+ * @return the module identifier removed
+ */
+ public ModuleIdentifier remove(int i)
+ {
+ return (ModuleIdentifier)this.list.remove(i);
+ }
+
+ /**
+ * Removes a module identifier from the list.
+ *
+ * @param m the module identifier to be removed
+ * @return the success
+ */
+ public boolean remove(ModuleIdentifier m)
+ {
+ return this.list.remove(m);
+ }
+
+ /**
+ * Returns the number of module identifiers.
+ *
+ * @return the size of the list
+ */
+ public int size()
+ {
+ return this.list.size();
+ }
+
+ /**
+ * Returns an array of module identifiers.
+ *
+ * @return the module identifiers
+ */
+ public ModuleIdentifier[] toArray()
+ {
+ Object[] objs = this.list.toArray();
+ ModuleIdentifier[] rtn = new ModuleIdentifier[objs.length];
+
+ System.arraycopy( objs, 0, rtn, 0, objs.length );
+
+ return rtn;
+ }
+} // ModuleIdentifierList
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleIdentifierList.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/05/24 19:21:34 lord
+ * Used system.arraycopy rather than manual method
+ *
+ * Revision 1.1 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/module/ModuleList.java b/src/uk/ac/man/bioinf/module/ModuleList.java
new file mode 100644
index 0000000..dbbf3b2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleList.java
@@ -0,0 +1,177 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+import java.util.List;
+
+
+/**
+ * To provide a list of modules in a type safe manor. This is
+ * basically a thin wrapper to list, specially targeted for modules.
+ *
+ *
+ * Created: Wed May 24 15:06:49 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleList.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ModuleList
+{
+ private List list;
+
+ public ModuleList(List list)
+ {
+ this.list = list;
+ }
+
+ /**
+ * Adds a module to the list.
+ *
+ * @param m the module
+ * @return the success of the addition
+ */
+ public boolean add(Module m)
+ {
+ return this.list.add(m);
+ }
+
+ /**
+ * Clear the list.
+ */
+ public void clear()
+ {
+ this.list.clear();
+ }
+
+ /**
+ * Returns whether a module is contained in this list.
+ *
+ * @param m the query module
+ * @return T/F exists
+ */
+ public boolean contains(Module m)
+ {
+ return this.list.contains(m);
+ }
+
+ /**
+ * Returns the module at a given index.
+ *
+ * @param i the index
+ * @return the module
+ */
+ public Module get(int i)
+ {
+ return (Module)this.list.get(i);
+ }
+
+ /**
+ * Returns the index of a module.
+ *
+ * @param m the module
+ * @return the index
+ */
+ public int indexOf(Module m)
+ {
+ return this.list.indexOf(m);
+ }
+
+ /**
+ * Returns whether the list is empty.
+ *
+ * @return T/F is the list empty
+ */
+ public boolean isEmpty()
+ {
+ return this.list.isEmpty();
+ }
+
+ /**
+ * Removes a module at a specific index.
+ *
+ * @param i the index of the module
+ * @return the module removed
+ */
+ public Module remove(int i)
+ {
+ return (Module)this.list.remove(i);
+ }
+
+ /**
+ * Removes a module from the list.
+ *
+ * @param m the module to be removed
+ * @return the success
+ */
+ public boolean remove(Module m)
+ {
+ return this.list.remove(m);
+ }
+
+ /**
+ * Returns the number of modules.
+ *
+ * @return the size of the list
+ */
+ public int size()
+ {
+ return this.list.size();
+ }
+
+ /**
+ * Returns an array of modules.
+ *
+ * @return the modules
+ */
+ public Module[] toArray()
+ {
+ Object[] objs = this.list.toArray();
+ Module[] rtn = new Module[objs.length];
+
+ for (int i = 0; i < rtn.length; i++) {
+ rtn[i] = (Module)objs[i];
+ }
+
+ return rtn;
+ }
+} // ModuleList
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleList.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/ModuleStorageStructure.java b/src/uk/ac/man/bioinf/module/ModuleStorageStructure.java
new file mode 100644
index 0000000..78c8af1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/ModuleStorageStructure.java
@@ -0,0 +1,197 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+import java.util.Arrays;
+
+
+/**
+ * ModuleStorageStructure.java
+ *
+ * Stores the module (if it exists), the context, the module
+ * configuration object and the required modules for one module
+ * identifier. This class is currently exclusively used in the
+ * DefaultModuleFactoryInstance.
+ *
+ * Created: Wed May 10 17:02:26 2000
+ *
+ * @author J Selley
+ * @version $Id: ModuleStorageStructure.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ModuleStorageStructure
+{
+ private Module module;
+ private Module[] requiredModules;
+ private ModuleContext context;
+ private Object config;
+ private ModuleIdentifier concrete;
+
+ public ModuleStorageStructure() {}
+
+ public ModuleStorageStructure(ModuleContext context)
+ {
+ this.context = context;
+ }
+
+ public ModuleStorageStructure(ModuleContext context, Object config)
+ {
+ this.context = context;
+ this.config = config;
+ }
+
+ public void setModule(Module module) throws ModuleException
+ {
+ if (this.module != null)
+ throw new
+ ModuleException("Module already defined in ModuleStorageStructure (" +
+ this + ")", ModuleExceptionType.MODULE_EXISTS);
+ else
+ this.module = module;
+ }
+
+ public Module getModule()
+ {
+ return this.module;
+ }
+
+ public void addRequiredModules(Module[] reqMods)
+ {
+ Module[] newModules;
+ int reqModsLength = (this.requiredModules != null) ? this.requiredModules.length : 0;
+ int givenModsLength = reqMods.length;
+
+ // generate correct sized array of new modules
+ newModules = new Module[reqModsLength + givenModsLength];
+
+ // put old required modules into new modules
+ for (int i = 0; i < reqModsLength; i++) {
+ newModules[i] = this.requiredModules[i];
+ }
+
+ // put given req. mods into the new modules
+ for (int i = reqModsLength; i < reqModsLength + givenModsLength; i++) {
+ newModules[i] = reqMods[i - reqModsLength];
+ }
+
+ // set new mods to req mods of this object
+ this.requiredModules = newModules;
+ }
+
+ public void addRequiredModule(Module reqMod)
+ {
+ // if there are previous required modules
+ if (this.requiredModules != null) {
+ // generate new modules array
+ Module[] newModules = new Module[this.requiredModules.length + 1];
+
+ // put previous required modules into new modules array
+ for (int i = 0; i < this.requiredModules.length; i++) {
+ newModules[i] = this.requiredModules[i];
+ }
+ // add the new req. mod. as the last module
+ newModules[this.requiredModules.length] = reqMod;
+
+ // set the new mods to the req mods
+ this.requiredModules = newModules;
+
+ } else {
+ this.requiredModules = new Module[1];
+ this.requiredModules[0] = reqMod;
+ }
+ }
+
+ public ModuleList getRequiredModules()
+ {
+ for( int i = 0; i < requiredModules.length; i++ ){
+ if( !requiredModules[ i ].isStarted() ){
+ requiredModules[ i ].runStart();
+ }
+ }
+
+ return new ModuleList( Arrays.asList( requiredModules ) );
+ }
+
+ public void setContext(ModuleContext context)
+ {
+ this.context = context;
+ }
+
+ public ModuleContext getContext()
+ {
+ return this.context;
+ }
+
+ public void setConfig(Object config)
+ {
+ this.config = config;
+ }
+
+ public Object getConfig()
+ {
+ return config;
+ }
+
+ public void setConcreteIdentifier( ModuleIdentifier ident )
+ {
+ this.concrete = ident;
+ }
+
+ public ModuleIdentifier getConcreteIdentifier()
+ {
+ return concrete;
+ }
+} // ModuleStorageStructure
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModuleStorageStructure.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.4 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.3 2000/05/30 16:27:56 lord
+ * Changes to ensure that modules are started.
+ *
+ * Revision 1.2 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ * Revision 1.1 2000/05/24 13:09:42 jns
+ * o initial coding of module package
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/NoSuchRequiredModule.java b/src/uk/ac/man/bioinf/module/NoSuchRequiredModule.java
new file mode 100644
index 0000000..2c00c11
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/NoSuchRequiredModule.java
@@ -0,0 +1,69 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+
+
+/**
+ * NoSuchRequiredModule.java
+ *
+ *
+ * Created: Mon Nov 13 15:24:02 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NoSuchRequiredModule.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NoSuchRequiredModule extends RuntimeException
+{
+
+ private ModuleIdentifier ident;
+ public NoSuchRequiredModule( ModuleIdentifier ident )
+ {
+ super( ident.toString() );
+ this.ident = ident;
+ }
+
+ public ModuleIdentifier getIdentifier()
+ {
+ return ident;
+ }
+} // NoSuchRequiredModule
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoSuchRequiredModule.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/13 15:34:42 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/module/NullModuleFactory.java b/src/uk/ac/man/bioinf/module/NullModuleFactory.java
new file mode 100644
index 0000000..985d8e5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/module/NullModuleFactory.java
@@ -0,0 +1,150 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.module; // Package name inserted by JPack
+import uk.ac.man.bioinf.module.Module;
+import uk.ac.man.bioinf.module.ModuleFactoryInstance;
+import uk.ac.man.bioinf.module.ModuleIdentifier;
+
+/**
+ * NullModuleFactory.java
+ *
+ * This class does precisely nothing, but in a very special way.....
+ *
+ * Created: Mon May 15 15:03:40 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NullModuleFactory.java,v 1.10 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NullModuleFactory implements ModuleFactoryInstance
+{
+ public boolean isModuleAvailable(ModuleIdentifier identifier)
+ {
+ return true;
+ }
+
+ public Module getModule(ModuleIdentifier identifier)
+ {
+ return null;
+ }
+
+ public ModuleList getRequiredModules(ModuleIdentifier identifier)
+ {
+ return null;
+ }
+
+ public void addIdentifier(ModuleIdentifier identifier)
+ {
+ }
+
+ public void addIdentifier(ModuleIdentifier[] identifiers)
+ {
+ }
+
+ public void addConfig(ModuleIdentifier identifier, Object config)
+ {
+ }
+
+ public Module load(ModuleIdentifier identifier)
+ {
+ return null;
+ }
+
+ public void setConfig( ModuleIdentifier mod, Object config )
+ {
+ }
+
+ public Object getConfig( ModuleIdentifier mod )
+ {
+ return null;
+ }
+
+ public ModuleIdentifier resolveModuleName( String moduleName )
+ {
+ return null;
+ }
+
+ public ModuleIdentifier resolveClassName( String className )
+ {
+ return null;
+ }
+
+ public void destroy()
+ {
+ }
+
+ public void setConcreteIdentifier
+ ( ModuleIdentifier abstractIdentifier, ModuleIdentifier concreteIdentifier )
+ {
+ }
+
+}// NullModuleFactory
+
+
+/*
+ * ChangeLog
+ * $Log: NullModuleFactory.java,v $
+ * Revision 1.10 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.9 2001/01/31 18:03:53 lord
+ * Changes due to removal of InterfaceIdentifier
+ *
+ * Revision 1.8 2001/01/26 17:13:55 lord
+ * Added get config method
+ *
+ * Revision 1.7 2000/09/15 16:31:23 lord
+ * Modifications to remove the ModuleFactory static class. This turned
+ * out to be rather limiting and also entirely unnecessary so I removed
+ * it.
+ *
+ * Revision 1.6 2000/07/18 11:12:14 lord
+ * Import rationalisation
+ *
+ * Revision 1.5 2000/06/16 09:40:07 jns
+ * o removed existence of BioInterface stuff, as it isn't really relevent here.
+ * Plus, in the pipe work is a reworking of what the BioInterface will
+ * represent and do.
+ *
+ * Revision 1.4 2000/05/30 16:28:12 lord
+ * resolveModuleName method
+ * resolveClassName method
+ *
+ * Revision 1.3 2000/05/24 19:22:09 lord
+ * Added addConfig method.
+ * Changed return type of load
+ *
+ * Revision 1.2 2000/05/24 15:38:37 jns
+ * o added ModuleList and MIList stuff and altered java to return module lists
+ * adn MILists rather than arrays.
+ *
+ * Revision 1.1 2000/05/15 14:11:36 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/AbstractEditableSequence.java b/src/uk/ac/man/bioinf/sequence/AbstractEditableSequence.java
new file mode 100644
index 0000000..0469305
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/AbstractEditableSequence.java
@@ -0,0 +1,173 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceEventType;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+
+
+/**
+ * AbstractEditableSequence.java
+ *
+ * This class provides trivial implementations of all of those methods
+ * which can be defined in terms of the others of the EditableSequence
+ * interface, and also ensures that the event handling occurs correctly
+ *
+ * Created: Fri Mar 3 12:11:49 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractEditableSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractEditableSequence extends AbstractMutableSequence
+ implements EditableSequence
+{
+ public AbstractEditableSequence( SequenceType type )
+ {
+ super( type );
+ }
+
+ protected abstract Element setElementAtQuietly( Element elem, int index );
+
+ public Element setElementAt( Element elem, int index ) throws SequenceVetoException
+ {
+ VetoableSequenceEvent event = new VetoableSequenceEvent( this, index, SequenceEventType.SET );
+ fireVetoableSequenceEvent( event );
+
+ Element retn = setElementAtQuietly( elem, index );
+
+ fireSequenceEvent( event );
+ return retn;
+ }
+
+ /**
+ * Provides a simple implementation of this method by iterating
+ * through the element array, and calling the super class
+ * method. Subclasses may override this to provide a more efficient implementation
+ * @param elem the elements to set
+ * @param index the index at which to start
+ */
+ public Element[] setElementAt( Element[] elem, int index ) throws SequenceVetoException
+ {
+ VetoableSequenceEvent event = new VetoableSequenceEvent( this, index, elem.length, SequenceEventType.SET );
+ fireVetoableSequenceEvent( event );
+
+ Element[] elems = new Element[ elem.length ];
+ for( int i = 0; i < elem.length; i++ ){
+ elems[ i ] = setElementAtQuietly( elem[ i ], index + i );
+ } //end for( i < length )
+
+ fireSequenceEvent( event );
+ return elems;
+ }
+
+ protected abstract void insertElementAtQuietly( Element elem, int index );
+
+ public void insertElementAt( Element elem, int index ) throws SequenceVetoException
+ {
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, SequenceEventType.INSERT );
+
+ fireVetoableSequenceEvent( event );
+ insertElementAtQuietly( elem, index );
+ fireSequenceEvent( event );
+ }
+
+
+ /**
+ * Provides a trivial implementation of this method by calling
+ * multiple single insert methods. Subclasses will almost definately
+ * find it more efficient to over ride this method!
+ * @param elem
+ * @param index
+ * @exception SequenceVetoException
+ */
+ public void insertElementAt( Element[] elem, int index ) throws SequenceVetoException
+ {
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, elem.length, SequenceEventType.INSERT );
+ fireVetoableSequenceEvent( event );
+
+ for( int i = 0; i < elem.length; i++ ){
+ insertElementAtQuietly( elem[ i ], index + i );
+ } //end for( i < length )
+
+ fireSequenceEvent( event );
+ }
+
+ /**
+ * Do the actual deletion but dont do any event signalling. This
+ * enables all the deletions to use this method without causing
+ * multiple events for deletions longer than one in length
+ * @param index the element to delete
+ * @return the element just deleted
+ */
+ protected abstract Element deleteElementAtQuietly( int index );
+
+ public Element deleteElementAt( int index ) throws SequenceVetoException
+ {
+ VetoableSequenceEvent event = new VetoableSequenceEvent( this, index, SequenceEventType.DELETE );
+ fireVetoableSequenceEvent( event );
+ Element retn = deleteElementAtQuietly( index );
+ fireSequenceEvent( event );
+
+ return retn;
+ }
+
+ public Element[] deleteElementAt( int index, int length ) throws SequenceVetoException
+ {
+ // inform any listeners what is about to happen
+ VetoableSequenceEvent event = new VetoableSequenceEvent( this, index, length, SequenceEventType.DELETE );
+ fireVetoableSequenceEvent( event );
+
+ // do the actual deletion via the quiet method
+ Element[] elem = new Element[ length ];
+ for( int i = 0; i < elem.length; i++ ){
+ elem[ i ] = deleteElementAtQuietly( index + i );
+ } //end for( i < elem.length )
+
+ // now inform any listeners of what has just happened
+ fireSequenceEvent( event );
+
+ return elem;
+ }
+} // AbstractEditableSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractEditableSequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/AbstractMutableSequence.java b/src/uk/ac/man/bioinf/sequence/AbstractMutableSequence.java
new file mode 100644
index 0000000..103884b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/AbstractMutableSequence.java
@@ -0,0 +1,114 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.MutableSequence;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceListenerSupport;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+
+
+/**
+ * AbstractMutableSequence.java
+ *
+ *
+ * Created: Thu Mar 2 20:20:02 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractMutableSequence.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractMutableSequence extends AbstractSequence
+ implements MutableSequence
+{
+ private SequenceListenerSupport supp = new SequenceListenerSupport();
+
+ public AbstractMutableSequence( SequenceType type )
+ {
+ super( type );
+ }
+
+ protected void fireVetoableSequenceEvent( VetoableSequenceEvent event ) throws SequenceVetoException
+ {
+ supp.fireVetoableSequenceEvent( event );
+ }
+
+ protected void fireSequenceEvent( SequenceEvent event )
+ {
+ supp.fireSequenceEvent( event );
+ }
+
+ protected boolean hasListeners()
+ {
+ return supp.hasListeners();
+ }
+
+ // implementation of uk.ac.man.bioinf.sequence.MutableSequence interface
+
+ public void addSequenceListener( SequenceListener listener )
+ {
+ supp.addSequenceListener( listener );
+ }
+
+ public void addVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ supp.addVetoableSequenceListener( listener );
+ }
+
+ public void removeSequenceListener( SequenceListener listener )
+ {
+ supp.removeSequenceListener( listener );
+ }
+
+ public void removeVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ supp.removeVetoableSequenceListener( listener );
+ }
+} // AbstractMutableSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractMutableSequence.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/09/15 16:32:51 lord
+ * Added hasListeners method
+ *
+ * Revision 1.2 2000/07/18 11:12:22 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/AbstractSequence.java b/src/uk/ac/man/bioinf/sequence/AbstractSequence.java
new file mode 100644
index 0000000..a710389
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/AbstractSequence.java
@@ -0,0 +1,170 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.Element;
+
+
+/**
+ * AbstractSequence.java
+ *
+ * Provides some of the methods for sequence. It assumes that the
+ * sequence is stored internally as a list of Residues and does all
+ * the mapping into chars.
+ *
+ * Created: Thu Mar 2 16:10:51 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractSequence.java,v 1.7 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractSequence implements Sequence
+{
+ private SequenceType type;
+
+ public AbstractSequence( SequenceType type )
+ {
+ this.type = type;
+ }
+
+ public SequenceType getSequenceType()
+ {
+ return type;
+ }
+
+ public Sequence getSubSequence( int position, int length )
+ {
+ checkRange( position );
+ checkRange( position + length - 1);
+
+ int end = position + length;
+
+ Element[] subsequence = new Element[ length ];
+ for( int i = position; i < end; i++ ){
+ subsequence[ i - position ] = getElementAt( i );
+ }
+
+ return new DefaultSequence( subsequence, getSequenceType() );
+ }
+
+ public char[] getSequenceAsChars()
+ {
+ Element[] seq = getSequenceAsElements();
+ char[] seqChars = new char[ seq.length ];
+ SequenceType type = getSequenceType();
+
+ for( int i = 0 ; i < seq.length ; i++ ){
+ seqChars[ i ] = seq[ i ].toChar();
+ } //end for( i < seq.length )
+ return seqChars;
+ }
+
+ public char getElementAtAsChar( int index )
+ {
+ return getElementAt( index ).toChar();
+ }
+
+ // some utility methods which may be useful for subclasses
+ /**
+ * Check if all these elements are of a valid type
+ * @throws InvalidSequenceTypeException if an element is not of a
+ * valid type
+ * @param elements the elements
+ * @param type the sequence type
+ */
+ protected void checkSequenceType( Element[] elements ) throws InvalidSequenceTypeException
+ {
+ // do some type checking to make sure all of the elements are of
+ // the correct type
+ for( int i = 0; i < elements.length; i++ ){
+ if( !type.isElement( elements[ i ] ) ){
+ throw new InvalidSequenceTypeException
+ ( "Element " + elements[ i ] + " at " + ( i + 1 ) + " is not part of the sequence type " +
+ type.toString() );
+ }
+ }
+ }
+
+ protected InvalidSequenceTypeException getSequenceTypeException( Element element )
+ {
+ return new InvalidSequenceTypeException
+ ( "Element " + element + " is not part of the sequence type " +
+ type.toString() );
+ }
+
+ protected void checkSequenceType( Element element ) throws InvalidSequenceTypeException
+ {
+ if( !type.isElement( element ) ){
+ throw getSequenceTypeException( element );
+ }
+ }
+
+ protected NoSuchSequenceElementException getSequenceIndexException( int index )
+ {
+ return new NoSuchSequenceElementException
+ ( "Attempt to access element at " + index + " in sequence " + this + " which does not exist" );
+ }
+
+ protected void checkRange( int index )
+ {
+ if( index < 1 || index > getLength() ){
+ throw getSequenceIndexException( index );
+ }
+ }
+} // AbstractSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequence.java,v $
+ * Revision 1.7 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.5 2000/03/23 19:51:36 lord
+ * Improved range checking for efficiency of access to elements
+ *
+ * Revision 1.4 2000/03/16 16:12:40 lord
+ * Fixed bug in subsequence ranges
+ *
+ * Revision 1.3 2000/03/14 19:42:51 jns
+ * o editing a problem that was to do with the translation of gapped indecies and
+ * ungapped indicies and vica-versa.
+ *
+ * Revision 1.2 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/03/02 17:45:55 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.java b/src/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.java
new file mode 100644
index 0000000..6b250fd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/ComplexEditableGappedSequence.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.EditableSequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.complex.ComplexSequence;
+
+
+/**
+ * ComplexEditableGappedSequence.java
+ *
+ *
+ * Created: Wed Dec 6 20:08:32 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexEditableGappedSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ComplexEditableGappedSequence
+ extends Sequence, MutableSequence, ComplexSequence, EditableSequence, GappedSequence
+{
+
+
+} // ComplexEditableGappedSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexEditableGappedSequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/13 16:33:17 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/DefaultEditableSequence.java b/src/uk/ac/man/bioinf/sequence/DefaultEditableSequence.java
new file mode 100644
index 0000000..3f1ef89
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/DefaultEditableSequence.java
@@ -0,0 +1,149 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import java.util.ArrayList;
+import java.util.Arrays;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+
+/**
+ * DefaultEditableSequence.java
+ *
+ *
+ * Created: Thu Mar 2 20:27:46 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultEditableSequence.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultEditableSequence extends AbstractEditableSequence
+ implements EditableSequence
+{
+ private ArrayList elements;
+ private Identifier ident;
+
+
+ public DefaultEditableSequence( Element[] elements, SequenceType type, Identifier identifier )
+ {
+ super( type );
+
+ checkSequenceType( elements );
+ this.ident = ident;
+
+ // the ArrayList constructor involves a cloning step, so changes
+ // will not percolate through to the underlying Element array. The
+ // Arrays.asList function (although it also returns an Object of
+ // underlying type ArrayList) does not do this on its own.
+ this.elements = new ArrayList( Arrays.asList( elements ) );
+ }
+
+ public DefaultEditableSequence( Sequence sequence, SequenceType type )
+ {
+ this( sequence.getSequenceAsElements(), type, new NoIdentifier() );
+ }
+
+ public DefaultEditableSequence( Sequence sequence )
+ {
+ this( sequence, sequence.getSequenceType() );
+ }
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+
+ public Element getElementAt( int index )
+ {
+ // -1!!! Dont you hate biologists!!!
+ return (Element)elements.get( index - 1 );
+ }
+
+ public int getLength()
+ {
+ return elements.size();
+ }
+
+ public Element[] getSequenceAsElements()
+ {
+ // get the elements, and make the destination array
+ Object[] elemObjs = elements.toArray();
+ Element[] elems = new Element[ elemObjs.length ];
+
+ // do the copy to array of appropriate type and return it
+ System.arraycopy( elemObjs, 0, elems, 0, elemObjs.length );
+ return elems;
+ }
+
+ protected Element setElementAtQuietly( Element elem, int index )
+ {
+ checkSequenceType( elem );
+ Element retn = getElementAt( index );
+ elements.set( index - 1, elem );
+ return retn;
+ }
+
+ protected void insertElementAtQuietly( Element elem, int index )
+ {
+ checkSequenceType( elem );
+ elements.add( index - 1, elem );
+ }
+
+ protected Element deleteElementAtQuietly( int index )
+ {
+ return (Element)elements.remove( index - 1 );
+ }
+} // DefaultEditableSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultEditableSequence.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/11/27 18:18:56 lord
+ * Fixed erroneous documentation
+ *
+ * Revision 1.4 2000/09/11 13:09:48 lord
+ * SequenceIdentifier renamed to Identifier
+ *
+ * Revision 1.3 2000/07/18 11:12:44 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.2 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/DefaultSequence.java b/src/uk/ac/man/bioinf/sequence/DefaultSequence.java
new file mode 100644
index 0000000..b6b4329
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/DefaultSequence.java
@@ -0,0 +1,134 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * DefaultSequence.java
+ *
+ *
+ * Created: Thu Mar 2 15:32:25 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultSequence.java,v 1.8 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultSequence extends AbstractSequence
+{
+ private Element[] elements;
+ private Identifier ident;
+
+
+ public DefaultSequence( Element[] elements, SequenceType type, Identifier ident )
+ {
+ super( type );
+ checkSequenceType( elements );
+ // decided not to make a clone at this point although this would
+ // probably have been the more secure thing to do, because its a
+ // bit of a waste
+ this.elements = elements;
+ this.ident = ident;
+ }
+
+ public DefaultSequence( Element[] elements, SequenceType type )
+ {
+ this( elements, type, new NoIdentifier() );
+ }
+
+ public DefaultSequence( Sequence seq, SequenceType type )
+ {
+ this( seq.getSequenceAsElements(), type );
+ }
+
+ public DefaultSequence( Sequence seq )
+ {
+ this( seq.getSequenceAsElements(), seq.getSequenceType() );
+ }
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+
+ public int getLength()
+ {
+ return elements.length;
+ }
+
+ public Element getElementAt( int index )
+ {
+ try{
+ return elements[ index - 1 ];
+ }
+ catch( ArrayIndexOutOfBoundsException ofbe ){
+ throw getSequenceIndexException( index );
+ }
+ }
+
+ public Element[] getSequenceAsElements()
+ {
+ // return a clone here so that changes to this dont percolate through
+ return (Element[])elements.clone();
+ }
+} // DefaultSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultSequence.java,v $
+ * Revision 1.8 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.7 2000/09/11 13:09:48 lord
+ * SequenceIdentifier renamed to Identifier
+ *
+ * Revision 1.6 2000/07/18 11:12:58 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.5 2000/05/18 17:05:19 lord
+ * Added support for passing in BioObject in cons
+ *
+ * Revision 1.4 2000/03/23 19:51:36 lord
+ * Improved range checking for efficiency of access to elements
+ *
+ * Revision 1.3 2000/03/16 16:13:48 lord
+ * Inserted range check in getElementAt
+ *
+ * Revision 1.2 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/03/02 17:47:43 lord
+ * Trivial non functional implementation that I needed to complete
+ * AbstractSequence
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/EditableSequence.java b/src/uk/ac/man/bioinf/sequence/EditableSequence.java
new file mode 100644
index 0000000..946532e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/EditableSequence.java
@@ -0,0 +1,125 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+
+/**
+ * EditableSequence.java
+ *
+ *
+ * Created: Wed Mar 1 19:39:40 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: EditableSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface EditableSequence extends MutableSequence
+{
+ /**
+ * Sets the value of the element at the specified index.
+ * @param element
+ * @param index
+ * @return the old value
+ * @throws NoSuchSequenceElementException if the element does not
+ * exist (index greater that length + 1 or less than 1)
+ * @throws SequenceVetoException if some listener doesnt like this
+ */
+ public Element setElementAt( Element element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public Element[] setElementAt( Element[] element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ /**
+ * Insert the element at the specified index. After insertion
+ * getElementAt( index ) will return element, and the sequence will
+ * be longer by one
+ * @param element the element to insert
+ * @param index the index at which to insert
+ */
+ public void insertElementAt( Element element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ /**
+ * Inserts the elements at this position. If the index is one longer
+ * than the length of the sequence the sequence will be extended.
+ * @param element the elements to insert
+ * @param index the index at which to insert
+ * @throws NoSuchSequenceElementException if the element does not
+ * exist, which will be the case if index is less than 1 or greater
+ * than sequence length + 1
+ */
+ public void insertElementAt( Element[] element, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ /**
+ * Delete the element at index.
+ * @param index the index to delete
+ * @return the element which has just been deleted
+ * @exception NoSuchSequenceElementException if index is less than 1
+ * or greater than the length of the sequence
+ */
+ public Element deleteElementAt( int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ /**
+ * Delete the elements starting at index for the specified length
+ * @param index the index to start at
+ * @param length the length to delete
+ * @return the elements just deleted
+ * @throws NoSuchSequenceElementException if the elements do not all
+ * exist, so if index is less than 1, or index + length is greater
+ * than the length of the sequence
+ */
+ public Element[] deleteElementAt( int index, int length )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+}// EditableSequence
+
+
+/*
+ * ChangeLog
+ * $Log: EditableSequence.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/11/27 18:18:35 lord
+ * Cosmetic
+ *
+ * Revision 1.3 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.2 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/03/01 20:16:55 lord
+ * Lots of stuff
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/Element.java b/src/uk/ac/man/bioinf/sequence/Element.java
new file mode 100644
index 0000000..4930ff8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/Element.java
@@ -0,0 +1,71 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+
+/**
+ * Element.java
+ *
+ * This interface defines an element within a sequence. Implementations
+ * of this will be immutable after definition. The interface is designed
+ * to be as thin as possible. Two equal elements should represent the
+ * same biological element.
+ *
+ * Created: Sat Feb 26 18:29:35 2000
+ *
+ * @author J Selley
+ * @version $Id: Element.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Element
+{
+ /**
+ * Returns a character representation of this element. This may be
+ * non-alphanumeric, and should be unique within a SequenceType.
+ * @see SequenceType
+ *
+ * @return the char representation
+ */
+ public char toChar();
+}// Element
+
+
+/*
+ * ChangeLog
+ * $Log: Element.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/02/26 18:42:26 jns
+ * Initial code for Element.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/EmptySequence.java b/src/uk/ac/man/bioinf/sequence/EmptySequence.java
new file mode 100644
index 0000000..bbe13f2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/EmptySequence.java
@@ -0,0 +1,114 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.types.EmptySequenceType;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * EmptySequence.java
+ *
+ *
+ * Created: Mon Feb 5 17:53:37 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: EmptySequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class EmptySequence implements Sequence
+{
+
+ private EmptySequence()
+ {
+ }
+
+ private static Sequence inst = new EmptySequence();
+ public static Sequence getInstance()
+ {
+ return inst;
+ }
+
+ private NoSuchSequenceElementException createException()
+ {
+ return new NoSuchSequenceElementException( "The empty sequence has no elements" );
+ }
+
+ // implementation of uk.ac.man.bioinf.sequence.Sequence interface
+ public Sequence getSubSequence(int param1, int param2) {
+ if( (param1 != 1) || (param2 != 1) ){
+ throw createException();
+ }
+ return this;
+ }
+
+ public SequenceType getSequenceType() {
+ return EmptySequenceType.getInstance();
+ }
+
+ private static Element[] noElements = new Element[ 0 ];
+ public Element[] getSequenceAsElements() {
+ return noElements;
+ }
+
+ private static char[] noChars = new char[ 0 ];
+ public char[] getSequenceAsChars() {
+ return noChars;
+ }
+
+ public int getLength() {
+ return 0;
+ }
+
+ public char getElementAtAsChar(int param1) {
+ throw createException();
+ }
+
+ public Element getElementAt(int param1) {
+ throw createException();
+ }
+
+ // implementation of uk.ac.man.bioinf.sequence.identifier.Identifiable interface
+ public Identifier getIdentifier() {
+ return new NoIdentifier();
+ }
+} // EmptySequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: EmptySequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/02/19 17:49:38 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.java b/src/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.java
new file mode 100644
index 0000000..9e16ab4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/InvalidSequenceTypeException.java
@@ -0,0 +1,64 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+
+/**
+ * InvalidSequenceTypeException.java
+ *
+ * Exception to signal that an attempt has been made to use a sequence
+ * of an invalid type.
+ *
+ * Created: Sat Feb 19 17:36:52 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: InvalidSequenceTypeException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class InvalidSequenceTypeException extends RuntimeException
+{
+ public InvalidSequenceTypeException( String message )
+ {
+ super( message );
+ }
+} // InvalidSequenceTypeException
+
+
+
+/*
+ * ChangeLog
+ * $Log: InvalidSequenceTypeException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/MutableSequence.java b/src/uk/ac/man/bioinf/sequence/MutableSequence.java
new file mode 100644
index 0000000..ec698a9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/MutableSequence.java
@@ -0,0 +1,69 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.event.SequenceEventProvider;
+
+
+/**
+ * MutableSequence.java
+ *
+ * A marker class to present a sequence which can be changed without
+ * the necessity for generating a new sequence. By extending
+ * SequenceEventProvider, the ability to listen to the sequence has
+ * been added.
+ *
+ * Created: Fri Feb 25 20:07:16 2000
+ *
+ * @author J Selley
+ * @version $Id: MutableSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface MutableSequence extends Sequence, SequenceEventProvider
+{
+
+}// MutableSequence
+
+
+/*
+ * ChangeLog
+ * $Log: MutableSequence.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/03/02 18:33:04 jns
+ * by the addition of SequenceEventProvider, this class now becomes a marker
+ * class for mutable sequences. The reason behind the creation of
+ * SequenceEventProvider is that the methods in the MSA class require the
+ * same names to access events of particular sequences.
+ *
+ * Revision 1.1.1.1 2000/02/26 16:51:33 jns
+ * The repository for the bioinf java classes
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.java b/src/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.java
new file mode 100644
index 0000000..bdb862c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/NoSuchSequenceElementException.java
@@ -0,0 +1,76 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+
+/**
+ * NoSuchSequenceElementException.java
+ *
+ *
+ * Created: Fri Mar 3 12:22:15 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NoSuchSequenceElementException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NoSuchSequenceElementException extends RuntimeException
+{
+ public NoSuchSequenceElementException()
+ {
+ super();
+ }
+
+ public NoSuchSequenceElementException( String message )
+ {
+ super( message );
+ }
+
+ public NoSuchSequenceElementException( Sequence seq, int index )
+ {
+ super( "Attempt to access element " + index + " of sequence " + seq + " which does not exist" );
+ }
+
+ public NoSuchSequenceElementException( String message, Sequence seq, int index )
+ {
+ super( message + ": " + seq + " at " + index );
+ }
+} // NoSuchSequenceElementException
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoSuchSequenceElementException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/Residue.java b/src/uk/ac/man/bioinf/sequence/Residue.java
new file mode 100644
index 0000000..1ee7176
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/Residue.java
@@ -0,0 +1,58 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+
+/**
+ * Residue.java
+ *
+ * An interface to represent entirely biological elements.
+ *
+ * Created: Mon Feb 28 12:23:49 2000
+ *
+ * @author J Selley
+ * @version $Id: Residue.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Residue extends Element
+{
+
+}// Residue
+
+
+/*
+ * ChangeLog
+ * $Log: Residue.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/02/28 14:06:09 jns
+ * Initial code.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/Sequence.java b/src/uk/ac/man/bioinf/sequence/Sequence.java
new file mode 100644
index 0000000..5be315d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/Sequence.java
@@ -0,0 +1,127 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.identifier.Identifiable;
+
+
+
+/**
+ * Sequence.java
+ *
+ * This interface is designed to model a biological sequence. It is
+ * non-specific in the manor in which a sequence may be implemented.
+ * The default implementation of this sequence will be imutable, and
+ * all sequence numbering will start at 1 <b>NOT</b> 0. This may be
+ * a set of rules worth following. For a mutable sequence, see the
+ * interface MutableSequence.
+ * @see MutableSequence
+ *
+ * Created: Fri Feb 25 19:21:55 2000
+ *
+ * @author J Selley
+ * @version $Id: Sequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Sequence extends Identifiable
+{
+ /**
+ * Returns a sub-sequence from the current sequence.
+ *
+ * @param from the initial index of the sub-sequence
+ * @param to the 'to' index of the sub-sequence
+ * @return the sub-sequence
+ */
+ public Sequence getSubSequence(int from, int length);
+
+ /**
+ * Returns the sequence as an array of characters.
+ *
+ * @return the sequence
+ */
+ public char[] getSequenceAsChars();
+
+ /**
+ * Returns the sequence as an array of elements.
+ *
+ * @return the sequence
+ */
+ public Element[] getSequenceAsElements();
+
+ /**
+ * Returns the character of an target element.
+ *
+ * @param index the location of the target element
+ * @return the element character
+ */
+ public char getElementAtAsChar(int index);
+
+ /**
+ * Returns an element at a given location.
+ *
+ * @param index the location of the target element
+ * @return the element
+ */
+ public Element getElementAt(int index);
+
+ /**
+ * Returns the type of sequence.
+ *
+ * @return the sequence type
+ */
+ public SequenceType getSequenceType();
+
+ /**
+ * Returns the length of the sequence.
+ *
+ * @return the length of the sequence
+ */
+ public int getLength();
+}// Sequence
+
+
+/*
+ * ChangeLog
+ * $Log: Sequence.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/07/18 11:13:08 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.3 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.2 2000/03/01 20:17:41 lord
+ * Updated for new interfaces
+ *
+ * Revision 1.1.1.1 2000/02/26 16:51:32 jns
+ * The repository for the bioinf java classes
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/SequenceException.java b/src/uk/ac/man/bioinf/sequence/SequenceException.java
new file mode 100644
index 0000000..0b7d423
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/SequenceException.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+
+/**
+ * SequenceException.java
+ *
+ *
+ * Created: Thu Mar 2 17:07:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceException extends RuntimeException
+{
+
+ public SequenceException( String message )
+ {
+ super( message );
+ }
+
+} // SequenceException
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/02 17:45:55 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/SequenceFactory.java b/src/uk/ac/man/bioinf/sequence/SequenceFactory.java
new file mode 100644
index 0000000..6c5eb9e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/SequenceFactory.java
@@ -0,0 +1,169 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file.
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.DefaultSequence;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.DNANucleotide;
+import uk.ac.man.bioinf.sequence.types.DNASequenceType;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * SequenceFactory provides a simple way into the Sequence API. It
+ * offers factory methods to create sequences from Strings and
+ * Characters. This, combined with the methods in the utility class
+ * <code>Sequences</code> is probably all that most users will need.
+ *
+ *
+ * Created: Tue Nov 14 18:06:37 2000
+ *
+ * @author Phillip Lord
+ * @author Crispin Miller
+ * @version $Id: SequenceFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $ */
+
+public class SequenceFactory {
+
+ protected static AminoAcid[] aa;
+
+ static {
+ AminoAcid[] all = AminoAcid.getAll();
+ aa = new AminoAcid[26];
+
+ for (int i = 0; i < all.length; i++)
+ aa[(int)all[i].toChar() - 65] = all[i];
+ }
+
+ /**
+ * Create a Sequence representing a protein sequence.
+ * @param proteinSequence a character array representing the residues in the sequence - see AminoAcid for more details
+ * @throws InvalidSequenceTypeException if the input sequence contains an invalid character.
+ */
+ public static Sequence getProteinSequence( char[] proteinSequence ) throws InvalidSequenceTypeException {
+ Element[] elements = new Element[ proteinSequence.length ];
+
+ for( int i = 0; i < proteinSequence.length; i++ ){
+ try{
+ elements[ i ] = aa[ Character.toUpperCase(proteinSequence[ i ]) - 65 ];
+ if( elements[ i ] == null ){
+ throw new InvalidSequenceTypeException( "No char " + proteinSequence[ i ] );
+ }
+ }
+ catch( ArrayIndexOutOfBoundsException aiob ){
+ System.out.println( (proteinSequence[ i ] - 65) );
+ throw new InvalidSequenceTypeException( "No char " + proteinSequence[ i ] );
+ }
+ }
+ return new DefaultSequence( elements, ProteinSequenceType.getInstance() );
+ }
+
+ /**
+ * Create a Sequence representing a protein sequence.
+ * @param proteinSequence represents the residues in the sequence - see AminoAcid for more details
+ * @throws InvalidSequenceTypeException if the input sequence contains an invalid character.
+ */
+ public static Sequence getProteinSequence( String proteinSequence ) throws InvalidSequenceTypeException {
+ Element[] elements = new Element[ proteinSequence.length() ];
+
+ for( int i = 0; i < proteinSequence.length(); i++ ){
+ try{
+ elements[ i ] = aa[ Character.toUpperCase(proteinSequence.charAt(i)) - 65 ];
+ if( elements[ i ] == null ){
+ throw new InvalidSequenceTypeException( "No char " + proteinSequence.charAt(i) );
+ }
+ }
+ catch( ArrayIndexOutOfBoundsException aiob ){
+ System.out.println( (proteinSequence.charAt(i) - 65) );
+ throw new InvalidSequenceTypeException( "No char " + proteinSequence.charAt(i) );
+ }
+ }
+ return new DefaultSequence( elements, ProteinSequenceType.getInstance() );
+ }
+
+ /**
+ * Create a Sequence representing a DNA sequence.
+ * @param dnaSequence represents the residues in the sequence - see Nucleotide for more details
+ * @throws InvalidSequenceTypeException if the input sequence contains an invalid character.
+ */
+ public static Sequence getDNASequence(char[] dnaSequence ) throws InvalidSequenceTypeException {
+ Element[] elements = new Element[ dnaSequence.length ];
+
+ for( int i = 0; i < dnaSequence.length; i++ ){
+
+ switch( Character.toUpperCase(dnaSequence[i]) ){
+
+ case 'A':
+ elements[ i ] = DNANucleotide.ADENOSINE;
+ break;
+
+ case 'C':
+ elements[ i ] = DNANucleotide.CYTOSINE;
+ break;
+
+ case 'G':
+ elements[ i ] = DNANucleotide.GUANINE;
+ break;
+
+ case 'T':
+ elements[ i ] = DNANucleotide.THIAMINE;
+ break;
+
+ default:
+ throw new InvalidSequenceTypeException( "Letter " + dnaSequence[ i ]
+ + " is not a valid part of a DNA Sequence" );
+ }
+ }
+
+ return new DefaultSequence( elements, DNASequenceType.getInstance() );
+ }
+
+ /**
+ * Create a Sequence representing a DNA sequence.
+ * @param dnaSequence represents the residues in the sequence - see Nucleotide for more details
+ * @throws InvalidSequenceTypeException if the input sequence contains an invalid character.
+ */
+ public static Sequence getDNASequence(String dnaSequence ) throws InvalidSequenceTypeException {
+ return getDNASequence( dnaSequence.toCharArray() );
+ }
+} // SequenceFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceFactory.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/11/22 18:58:25 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/SequenceType.java b/src/uk/ac/man/bioinf/sequence/SequenceType.java
new file mode 100644
index 0000000..da41b4e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/SequenceType.java
@@ -0,0 +1,153 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+
+
+/**
+ * SequenceType.java
+ *
+ * An interface to represent the type of a sequence (e.g: Protein, DNA).
+ *
+ * Created: Fri Feb 25 20:12:45 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceType.java,v 1.7 2001/05/08 17:47:31 lord Exp $
+ */
+
+public interface SequenceType
+{
+ /**
+ * Returns the number of elements in this sequence type.
+ * @return the number of elements
+ */
+ public int size();
+
+ /**
+ * This method is present as a performance enhancement. For every
+ * Element this method should return a unique and repeatable int,
+ * starting at 0 and ending at size() - 1 for all possible
+ * Elements. This enables the Element to be used as an index for an
+ * array which in turn allows implementation of efficient look up
+ * tables, rather than using a hashtable.
+ *
+ * @param element the element
+ * @return a int
+ */
+ public int getIntForElement( Element element );
+
+ /**
+ * The inverse of the method getIntForElement.
+ * @param index a value of type 'int'
+ * @return a value of type 'Element'
+ */
+ public Element getElementForInt( int index );
+
+ /**
+ * Returns all the elements available in this sequence type.
+ * This array should be freely modifiable, and changes should not
+ * percolate backwards iunto the internal data of the sequence
+ * type.
+ *
+ * @return the elements
+ */
+ public Element[] getElements();
+
+ /**
+ * Returns the human readable form of this sequence type.
+ *
+ * @return the name
+ */
+ public String getName();
+
+ /**
+ * Returns a boolean as to whether the specified element is part
+ * of this sequence type.
+ *
+ * @param element the element
+ * @return whether an element
+ */
+ public boolean isElement(char element);
+
+ /**
+ * Returns a boolean as to whether the specified element is part
+ * of this sequence type.
+ *
+ * @param element the element
+ * @return whether an element
+ */
+ public boolean isElement(Element element);
+
+ /**
+ * Returns a boolean as to whether the specified elements are part
+ * of this sequence type.
+ *
+ * @param elements the elements
+ * @return whether elements
+ */
+ public boolean isElement(char[] elements);
+
+ /**
+ * Returns a boolean as to whether the specified elements are part
+ * of this sequence type.
+ *
+ * @param elements the elements
+ * @return whether elements
+ */
+ public boolean isElement(Element[] elements);
+}// SequenceType
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceType.java,v $
+ * Revision 1.7 2001/05/08 17:47:31 lord
+ * Cosmetic changes
+ *
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/10/03 17:14:20 lord
+ * Added documentation
+ *
+ * Revision 1.4 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.3 2000/06/27 16:05:09 lord
+ * Added getIntForElement and getElementForInt methods
+ *
+ * Revision 1.2 2000/06/13 11:00:25 lord
+ * Added size method
+ *
+ * Revision 1.1 2000/02/26 16:51:33 jns
+ * Initial revision
+ *
+ * Revision 1.1 2000/02/26 16:51:33 jns
+ * Initial revision
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/Sequences.java b/src/uk/ac/man/bioinf/sequence/Sequences.java
new file mode 100644
index 0000000..53f0b3d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/Sequences.java
@@ -0,0 +1,339 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.complex.ComplexElement;
+import uk.ac.man.bioinf.sequence.complex.ComplexElementFactory;
+import uk.ac.man.bioinf.sequence.complex.ComplexSequence;
+import uk.ac.man.bioinf.sequence.complex.GappedComplexSequence;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * Sequences.java
+ *
+ *
+ * Created: Tue Mar 14 13:43:59 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Sequences.java,v 1.15 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class Sequences
+{
+ private Sequences()
+ {
+ //no objects!!
+ }
+
+ /**
+ * Returns a GappedSequence with the Elements in the array, which
+ * can included gaps. All other elements must be contained in the
+ * SequenceType however.
+ * @param elements the elements
+ * @param type the sequence type
+ * @return the sequence
+ */
+ public static GappedSequence getElementsAsGappedSequence( Element[] elements, SequenceType type )
+ {
+ return DefaultGappedSequence.getElementsAsGappedSequence( elements, type );
+ }
+
+ /**
+
+ * Returns a GappedSequence with the Elements in the array, which
+ * can included gaps. All other elements must be contained in the
+ * SequenceType however.
+ *
+ * @param elements the elements
+ * @param type the sequence type
+ * @param iface the biointerface
+ * @return the sequence
+
+ */
+ public static GappedSequence getElementsAsGappedSequence
+ (Element[] elements, SequenceType type, Identifier ident )
+ {
+ return DefaultGappedSequence.getElementsAsGappedSequence(elements, type, ident );
+ }
+
+ public static Sequence getElementsAsSequence( Element[] elements, SequenceType type )
+ {
+ return new DefaultSequence( elements, type );
+ }
+
+ public static Sequence getElementsAsSequence
+ ( Element[] elements, SequenceType type, Identifier ident )
+ {
+ return new DefaultSequence( elements, type, ident );
+ }
+
+ /**
+ * This removes all of the leading gaps from a gapped sequence, and
+ * then returns the number of gaps removed.
+ * @param seq the sequence to chomp
+ * @return the number of gaps
+ */
+ public static int chompLeadingGaps( GappedSequence seq ) throws SequenceVetoException
+ {
+ int i = 0;
+ // (PENDING:- PL) Quick and dirty implementation. Should be
+ // possible to do this with a single method invocation.
+ while( seq.getLength() > 1 && seq.getGappedElementAt( 1 ) == Gap.GAP ){
+ seq.deleteGapAt( 1 );
+ i++;
+ }
+
+ return i;
+ }
+
+ /**
+ * Removes and returns the number of trailing gaps off a gapped
+ * sequence.
+ *
+ * @param seq the sequence
+ * @return the number of gaps
+ */
+ public static int chompTrailingGaps(GappedSequence seq)
+ throws SequenceVetoException
+ {
+ int numberGapsRemoved = 0;
+
+ while (seq.getGappedElementAt(seq.getGappedLength()) == Gap.GAP) {
+ seq.deleteGapAt(seq.getGappedLength());
+ numberGapsRemoved++;
+ }
+
+ return numberGapsRemoved;
+ }
+
+ /**
+ * Returns the number of gaps upstream from a given index in the
+ * given sequence. If the index is out of bounds, it returns zero.
+ * @param index the location in the sequence to start counting
+ * upstream from
+ * @param seq the sequence
+ * @return the number of gaps upstream for the given location
+ */
+ public static int getNumberGapsUpstreamFrom(int index, GappedSequence seq)
+ {
+ // N.B. Sequence numbers start at 1 *NOT* 0
+ if ((index < 1) || (index > seq.getGappedLength()))
+ return 0;
+
+ int numberGaps = 0;
+ // while we are still in the sequence, move from index upstream
+ // until we meet a non-gap element, incrementing the number of
+ // gaps
+ while ((numberGaps + index < seq.getGappedLength()) &&
+ (seq.getGappedElementAt(numberGaps + index) == Gap.gap))
+ numberGaps++;
+
+ // return the calculated number of gaps
+ return numberGaps;
+ }
+
+ /**
+ * Returns the number of gaps downstream from a given index in the
+ * given sequence. If the index is out of bounds, it returns zero.
+ * @param index the location in the sequence to start counting
+ * downstream from
+ * @param seq the sequence
+ * @return the number of gaps downstream for the given location
+ */
+ public static int getNumberGapsDownstreamFrom(int index, GappedSequence seq)
+ {
+ // N.B. Sequence numbers start at 1 *NOT* 0
+ if ((index < 1) || (index > seq.getGappedLength()))
+ return 0;
+
+ int numberGaps = 0;
+ // while we are still in the sequence, move from index, downstream
+ // until we meet a non-gap element, incrementing the number of
+ // gaps
+ while ((index - numberGaps > 1) &&
+ (seq.getGappedElementAt(index - numberGaps) == Gap.gap))
+ numberGaps++;
+
+ // return the calculated number of gaps
+ return numberGaps;
+ }
+
+ public static String getSequenceAsString( Sequence seq )
+ {
+ return String.valueOf( seq.getSequenceAsChars() );
+ }
+
+ public static String getSubSequenceAsString( Sequence seq, int start, int length )
+ {
+ return getSequenceAsString( seq.getSubSequence( start, length ) );
+ }
+
+ public static String getGappedSequenceAsString( GappedSequence seq )
+ {
+ return String.valueOf( seq.getGappedSequenceAsChars() );
+ }
+
+ public static String getGappedSubSequenceAsString( GappedSequence seq, int start, int length )
+ {
+ return getGappedSequenceAsString( seq.getGappedSubSequence( start, length ) );
+ }
+
+ public static String getElementsAsString( Element[] elem )
+ {
+ char[] chrs = new char[ elem.length ];
+ for( int i = 0; i < chrs.length; i++ ){
+ chrs[ i ] = elem[ i ].toChar();
+ }
+ return String.valueOf( chrs );
+ }
+
+ public static String getComplexSequenceAsString( ComplexSequence seq )
+ {
+ return String.valueOf( seq.getComplexSequenceAsChars() );
+ }
+
+ public static ComplexElement[] getResiduesAsComplexElements( Residue[] elements )
+ {
+ ComplexElement[] complex = new ComplexElement[ elements.length ];
+
+ for( int i = 0; i < elements.length; i++ ){
+ complex[ i ] = ComplexElementFactory.getComplexElement( elements[ i ] );
+ }
+
+ return complex;
+ }
+
+
+ public static void printAlignment( SequenceAlignment align )
+ {
+ System.out.print( "Alignment " + "Size: " + align.getNumberSequences() + " Length: " + align.getLength() );
+ System.out.println();
+
+
+ for( int i = 1; i < align.getNumberSequences() + 1; i++ ){
+ GappedSequence seq = align.getSequenceAt( i );
+
+ System.out.println( "Sequence " + i + ": " + seq.getIdentifier().getTitle() + " Length: " + seq.getGappedLength() );
+ for( int j = 0; j < align.getInset( i ); j++ ){
+ System.out.print( "+" );
+ }
+
+ printSequence( seq );
+ }
+ }
+
+ public static void printSequence( GappedSequence seq )
+ {
+ System.out.println( getGappedSequenceAsString( seq ) );
+ }
+
+ public static void printSequence( ComplexSequence seq )
+ {
+ System.out.println( getComplexSequenceAsString( seq ) );
+ }
+
+ public static void printSequence( GappedComplexSequence seq )
+ {
+ printSequence( (GappedSequence)seq );
+ printSequence( (ComplexSequence)seq );
+ }
+
+ public static void printSequence( Sequence seq )
+ {
+ System.out.println( getSequenceAsString( seq ) );
+ }
+
+ public static void printElements( Element[] elem )
+ {
+ System.out.println( getElementsAsString( elem ) );
+ }
+} // Sequences
+
+
+
+/*
+ * ChangeLog
+ * $Log: Sequences.java,v $
+ * Revision 1.15 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.14 2001/02/19 17:46:49 lord
+ * Some new methods
+ *
+ * Revision 1.13 2000/12/13 16:33:55 lord
+ * ComplexElement and ComplexSequence support methods
+ *
+ * Revision 1.12 2000/11/27 18:18:19 lord
+ * Added methods to print ComplexSequences
+ *
+ * Revision 1.11 2000/11/02 14:52:08 jns
+ * o added functions to calculate the gaps from a specific gapped
+ * locaiton, upstream and downstream.
+ *
+ * Revision 1.10 2000/09/11 13:09:48 lord
+ * SequenceIdentifier renamed to Identifier
+ *
+ * Revision 1.9 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.8 2000/07/18 12:32:52 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.7 2000/06/22 16:02:26 jns
+ * o added a chompTrailingGaps function to complement the chompLeadingGaps
+ * function.
+ *
+ * Revision 1.6 2000/06/13 10:59:46 lord
+ * Now more descriptive when printing out
+ *
+ * Revision 1.5 2000/06/08 12:34:54 jns
+ * o added method to get a gapped sequence as elements *with* the biointerface
+ * supplied. It is merely over-riding the previous method which didn't offer
+ * addition of the biointerface - even though it exists in the default gapped
+ * sequence.
+ *
+ * Revision 1.4 2000/06/05 14:24:06 lord
+ * Added print alignment method
+ *
+ * Revision 1.3 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.2 2000/05/18 17:04:48 lord
+ * A couple of new methods
+ *
+ * Revision 1.1 2000/03/14 15:11:46 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.java b/src/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.java
new file mode 100644
index 0000000..31b519c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/AbstractGappedSequence.java
@@ -0,0 +1,201 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.AbstractMutableSequence;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.SequenceEventType;
+import uk.ac.man.bioinf.sequence.NoSuchSequenceElementException;
+
+
+/**
+ * AbstractGappedSequence.java
+ *
+ *
+ * Created: Sat Mar 4 12:17:02 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractGappedSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractGappedSequence extends AbstractMutableSequence
+ implements GappedSequence
+{
+ public AbstractGappedSequence( SequenceType type )
+ {
+ super( type );
+ }
+
+ protected abstract void insertGapAtQuietly( int index );
+
+ public void insertGapAt( int index ) throws SequenceVetoException
+ {
+ boolean fireEventP = hasListeners();
+
+ if( fireEventP ){
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, SequenceEventType.GAPINSERT );
+
+ fireVetoableSequenceEvent( event );
+ insertGapAtQuietly( index );
+ fireSequenceEvent( event );
+ }
+ else{
+ // premature optimization is the root of all evil.
+ insertGapAtQuietly( index );
+ }
+ }
+
+ public void insertGapAt( int index, int length ) throws SequenceVetoException
+ {
+ boolean fireEventP = hasListeners();
+
+ if( fireEventP ){
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, length, SequenceEventType.GAPINSERT );
+ fireVetoableSequenceEvent( event );
+
+ for( int i = 0; i < length; i++ ){
+ insertGapAtQuietly( index + i );
+ } //end for( i < length )
+
+ fireSequenceEvent( event );
+ }
+ else{
+ // premature optimization is the root of all evil.
+ for( int i = 0; i < length; i++ ){
+ insertGapAtQuietly( index + i );
+ } //end
+ }
+
+ }
+
+ protected abstract void deleteGapAtQuietly( int index );
+
+ public void deleteGapAt( int index ) throws SequenceVetoException
+ {
+ // delegate function
+ this.deleteGapAt(index, 1);
+ }
+
+ public void deleteGapAt( int index, int length ) throws SequenceVetoException
+ {
+ boolean fireEventP = hasListeners();
+
+ if( fireEventP ){
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, length, SequenceEventType.GAPDELETE );
+ fireVetoableSequenceEvent( event );
+
+ for( int i = 0; i < length; i++ ){
+ deleteGapAtQuietly( index );
+ } //end for( i < length )
+
+ fireSequenceEvent( event );
+ }
+ else{
+ for( int i = 0; i < length; i++ ){
+ deleteGapAtQuietly( index + i );
+ } //end for( i < length )
+ }
+ }
+
+ public char getGappedElementAtAsChar( int index )
+ {
+ return getGappedElementAt( index ).toChar();
+ }
+
+ public char[] getGappedSequenceAsChars()
+ {
+ char[] retn = new char[ getGappedLength() ];
+
+ Element[] elements = getGappedSequenceAsElements();
+
+ for( int i = 0; i < elements.length; i++ ){
+ retn[ i ] = elements[ i ].toChar();
+ } //end for( i < elements.length )
+
+ return retn;
+ }
+
+
+ // protected utility methods
+ protected void checkGappedRange( int index )
+ {
+ if( index < 1 || index > getGappedLength() ){
+ throw getGappedSequenceIndexException( index );
+ }
+ }
+
+ protected void checkGappedRangeForInsert( int index )
+ {
+ if( index < 1 || index > getGappedLength() + 1 ){
+ throw new NoSuchSequenceElementException( "Attempt to insert gapped element " +
+ index + " in sequence " + this + " illegally" );
+ }
+ }
+
+ protected NoSuchSequenceElementException getGappedSequenceIndexException( int index )
+ {
+ return new NoSuchSequenceElementException( "Attempt to access gapped element " +
+ index + " in sequence " + this + " which doesnt exist" );
+ }
+} // AbstractGappedSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractGappedSequence.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/11/02 14:55:17 jns
+ * o made deleteGapAt(int) call its sister deleteGapAt(int, int) to save
+ * on code usage
+ * o made deleteGapAt actually function correctly - previously I had
+ * forgotten that the delete function is as the DEL key works, not as the
+ * BACK_SPACE key works (i.e., deletion works from left -> right, not
+ * right -> left).
+ *
+ * Revision 1.3 2000/09/15 16:34:14 lord
+ * Now only instantiates events when there are actually listeners. This
+ * small change can actually save the creation of a vast number of events
+ * in practice, as many gaps are often removed when parsing an
+ * SequenceAlignment from file
+ *
+ * Revision 1.2 2000/03/23 19:51:36 lord
+ * Improved range checking for efficiency of access to elements
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.java b/src/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.java
new file mode 100644
index 0000000..5fc9831
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/AbstractSequenceAlignment.java
@@ -0,0 +1,471 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceEventType;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceListenerSupport;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+
+
+/**
+ * AbstractSequenceAlignment.java
+ *
+ * An abstract class to extend for the basic definition of a multiple
+ * sequence alignment. This class basically ensures listener handling.
+ *
+ * Created: Mon Feb 21 13:02:10 2000
+ *
+ * @author J Selley
+ * @version $Id: AbstractSequenceAlignment.java,v 1.13 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractSequenceAlignment
+ implements SequenceAlignment, VetoableSequenceListener
+{
+
+ protected abstract void setLengthQuietly( int length );
+
+ /**
+ * Adds a sequence to the alignment, quietly, without notifying
+ * listeners.
+ * @param sequence the sequence
+ * @param inset the inset of the sequence
+ */
+ protected abstract void addSequenceQuietly(GappedSequence sequence, int inset);
+
+ public SequenceAlignment getSubAlignment( SequenceAlignmentRectangle rect )
+ {
+ return getSubAlignment( rect.getX(), rect.getWidth(), rect.getY(), rect.getHeight() );
+ }
+
+ /**
+ * Adds a sequence to the alignment. This action can be vetoed by a
+ * listener.
+ * @param seq the sequence
+ * @exception AlignmentVetoException veto to the addition
+ */
+ public void addSequence(GappedSequence seq, int inset)
+ throws AlignmentVetoException
+ {
+ // signal listeners of the intention to add a sequence
+ msls.fireVetoableAlignmentEvent
+ (new VetoableAlignmentEvent(this, this.getNumberSequences() + 1,
+ AlignmentEventType.INSERT));
+
+ // add the sequence
+ addSequenceQuietly(seq, inset);
+
+ // check to see whether this has caused an increase in the overall
+ // length of the Alignment and signal the subclass implementation
+ // if it has.
+ ensureLengthIncrease( seq.getGappedLength() + inset, getNumberSequences() );
+
+ // notify listeners that the removal has taken place successfully
+ msls.fireAlignmentEvent
+ (new AlignmentEvent(this, this.getNumberSequences() + 1,
+ AlignmentEventType.INSERT));
+ }
+
+ /**
+ * Calls addSequence on every sequence in the supplied
+ * alignment. This basically provides a simple shortcut method.
+ *
+ * @param align the alignment of sequences to be added
+ * @exception AlignmentVetoException veto to the addition - this can
+ * be sequence based as well as alignment based
+ */
+ public void addSequence(SequenceAlignment align)
+ throws AlignmentVetoException
+ {
+ /* (PENDING: JNS) 11.12.00 This may be overly complex, and result
+ * in a lot of alignment event firing. i.e., this may need
+ * cleaning up.
+ */
+ // signal listeners of intention to add the alignment
+ msls.fireVetoableAlignmentEvent
+ (new VetoableAlignmentEvent(this, this.getNumberSequences() +
+ align.getNumberSequences(),
+ AlignmentEventType.INSERT));
+
+ // for each sequence in the given alignment...
+ for (int i = 0; i < align.getNumberSequences(); i++) {
+ // add the sequence via call to addSequence
+ addSequence(align.getSequenceAt(i), align.getInset(i));
+ }
+
+ // notify listeners that the insertion has taken place
+ // successfully
+ msls.fireAlignmentEvent
+ (new AlignmentEvent(this, this.getNumberSequences() +
+ align.getNumberSequences(),
+ AlignmentEventType.INSERT));
+ }
+
+ /**
+ * Remove a sequence from the alignment, quietly, without notifying
+ * listeners.
+ * @param seqIndex the sequence index
+ * @return the sequence
+ */
+ protected abstract GappedSequence removeSequenceQuietly(int seqIndex);
+
+ /**
+ * Removes a sequence from the alignment. This action can be veetoed
+ * by a listener.
+ * @param seqIndex the sequence index
+ * @return the sequence
+ * @exception AlignmentVetoException veto to the removal
+ */
+ public GappedSequence removeSequence(int seqIndex)
+ throws AlignmentVetoException
+ {
+ // signal listeners of the intention to remove a sequence
+ msls.fireVetoableAlignmentEvent
+ (new VetoableAlignmentEvent(this, seqIndex, AlignmentEventType.DELETE));
+
+ // remove the sequence
+ GappedSequence rtn = removeSequenceQuietly(seqIndex);
+
+ // notify listeners that the removal has taken place successfully
+ msls.fireAlignmentEvent
+ (new AlignmentEvent(this, seqIndex, AlignmentEventType.DELETE));
+
+ // return the sequence
+ return rtn;
+ }
+
+ /**
+ * Set the inset (or number of preceeding gaps) in a sequence, quietly
+ * without notifying listeners.
+ *
+ * @param seqIndex the sequence index
+ * @param inset the inset or preceeding number of gaps
+ */
+ protected abstract void setInsetQuietly(int seqIndex, int inset);
+
+
+ /**
+ * Set the inset (or number of preceeding gaps) in a sequence.
+ *
+ * @param seqIndex the sequence index
+ * @param inset the inset or preceeding number of gaps
+ */
+ public void setInset(int seqIndex, int inset)
+ throws AlignmentVetoException
+ {
+ // bomb out if no change has occurred
+ if( inset == getInset( seqIndex ) ) return;
+
+ // signal listeners of the change to occur
+ msls.fireVetoableAlignmentEvent
+ (new VetoableAlignmentEvent(this, seqIndex, AlignmentEventType.INSET_CHANGE));
+
+ // we may need to signal that the length has increased.
+ // (PENDING:- PL) We should also check here that length has not decreased!!!
+ if( inset > getInset( seqIndex ) ){
+ ensureLengthIncrease( inset + getSequenceAt( seqIndex ).getGappedLength(), seqIndex );
+ }
+ else{
+ ensureLengthDecrease();
+ }
+
+ // do the insertion
+ setInsetQuietly(seqIndex, inset);
+ // notify listeners of the change
+ msls.fireAlignmentEvent
+ (new AlignmentEvent(this, seqIndex, AlignmentEventType.INSET_CHANGE));
+ }
+
+ /**
+ * This method checks to see whether a length increase has occurred,
+ * and if it has signals events, and changes the length
+ * @param newLength what is potentially the new length if its long
+ * enough!
+ * @param seqIndex the sequence which may have caused the change or
+ * 0 if not known
+ */
+ private void ensureLengthIncrease( int newLength, int seqIndex ) throws AlignmentVetoException
+ {
+ if( newLength > getLength() ){
+ fireVetoableAlignmentEvent
+ ( new VetoableAlignmentEvent( this, seqIndex, AlignmentEventType.LENGTH_CHANGE ) );
+ setLengthQuietly( newLength );
+ fireAlignmentEvent
+ ( new AlignmentEvent( this, seqIndex, AlignmentEventType.LENGTH_CHANGE ) );
+ }
+ }
+
+ /**
+ * This method checks to see whether a length decrease has
+ * occurred. At the moment it exhaustively checks through all of the
+ * sequences because I can not think of an easier way of doing
+ * this.
+ */
+ private void ensureLengthDecrease() throws AlignmentVetoException
+ {
+ int longest = 0;
+ for( int i = 1; i < getNumberSequences() + 1; i++ ){
+ int currLength = getSequenceAt( i ).getGappedLength() + getInset( i );
+
+ if( currLength > longest ) longest = currLength;
+ }
+
+ if( longest != getLength() ){
+ fireVetoableAlignmentEvent
+ ( new VetoableAlignmentEvent( this, 0, AlignmentEventType.LENGTH_CHANGE ) );
+ setLengthQuietly( longest );
+ fireAlignmentEvent
+ ( new AlignmentEvent( this, 0, AlignmentEventType.LENGTH_CHANGE ) );
+ }
+ }
+
+ // alignment event production
+ private AlignmentListenerSupport msls = new AlignmentListenerSupport();
+
+ protected void fireAlignmentEvent( AlignmentEvent event )
+ {
+ msls.fireAlignmentEvent( event );
+ }
+
+ protected void fireVetoableAlignmentEvent( VetoableAlignmentEvent event )
+ throws AlignmentVetoException
+ {
+ msls.fireVetoableAlignmentEvent( event );
+ }
+
+ /**
+ * Delegates to the AlignmentListenerSupport object, the addition
+ * of a Multiple Sequence (MS) listener.
+ *
+ * @param listener a MS listener
+ */
+ public void addAlignmentListener(AlignmentListener listener)
+ {
+ if (listener != null) msls.addAlignmentListener(listener);
+ }
+
+ /**
+ * Delegates to the AlignmentListenerSupport the removal of the
+ * MS listener.
+ *
+ * @param listener the MS listener to be removed
+ */
+ public void removeAlignmentListener(AlignmentListener listener)
+ {
+ if (listener != null) msls.removeAlignmentListener(listener);
+ }
+
+ /**
+ * Delegates to the AlignmentListenerSupport the addition of a
+ * vetoable MS listener.
+ *
+ * @param listener a vetoable MS listener to be added
+ */
+ public void addVetoableAlignmentListener
+ (VetoableAlignmentListener listener)
+ {
+ if (listener != null) addVetoableAlignmentListener(listener);
+ }
+
+ /**
+ * Delegates to the AlignmentListenerSupport the removal of the
+ * vetoable MS listener.
+ *
+ * @param listener the vetoable MS listener to be removed
+ */
+ public void removeVetoableAlignmentListener
+ (VetoableAlignmentListener listener)
+ {
+ if (listener != null) removeVetoableAlignmentListener(listener);
+ }
+
+ // SequenceEventProvider support
+ private SequenceListenerSupport supp = new SequenceListenerSupport();
+
+ private void fireVetoableSequenceEvent( VetoableSequenceEvent event ) throws SequenceVetoException
+ {
+ supp.fireVetoableSequenceEvent( event );
+ }
+
+ private void fireSequenceEvent( SequenceEvent event )
+ {
+ supp.fireSequenceEvent( event );
+ }
+
+ public void addSequenceListener( SequenceListener listener )
+ {
+ supp.addSequenceListener( listener );
+ }
+
+ public void addVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ supp.addVetoableSequenceListener( listener );
+ }
+
+ public void removeSequenceListener( SequenceListener listener )
+ {
+ supp.removeSequenceListener( listener );
+ }
+
+ public void removeVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ supp.removeVetoableSequenceListener( listener );
+ }
+
+ // implementation of listener
+ public void vetoableChangeOccurred( VetoableSequenceEvent event )
+ throws SequenceVetoException
+ {
+ fireVetoableSequenceEvent( event );
+ }
+
+ // this sequence is used to cache the furthest right sequence
+ //private GappedSequence longestSequence = null;
+ public void changeOccurred( SequenceEvent event )
+ {
+ // fire the event to this objects listeners
+ fireSequenceEvent( event );
+
+ /* (PENDING: JNS) 25.10.00 May have to revise this - particularly
+ * whether or not to throw a vetoable event
+ */
+ // update the length if necessary for an insert
+ if ((event.getType() == SequenceEventType.GAPINSERT) &&
+ ((((GappedSequence)event.getSource()).getGappedLength() +
+ getInset(getSequenceIndex((GappedSequence)event.getSource()))) >
+ getLength())) {
+ setLengthQuietly(((GappedSequence)event.getSource()).getGappedLength() +
+ getInset(getSequenceIndex((GappedSequence)event.
+ getSource())));
+ // fire a further event to signal the length has changed
+ fireAlignmentEvent(new AlignmentEvent
+ (this, getSequenceIndex((GappedSequence)event.getSource()),
+ AlignmentEventType.LENGTH_CHANGE));
+ }
+
+ // update the length when removing gaps
+ if (event.getType() == SequenceEventType.GAPDELETE) {
+ GappedSequence source = (GappedSequence)event.getSource();
+
+ try{
+ // (PENDING:- PL) Horrible code. This all needs changing to a
+ // better system.
+ ensureLengthDecrease();
+ }
+ catch( Exception exp ){
+ }
+
+
+ // if ((longestSequence == null) ||
+// (source == longestSequence) ||
+// ((source.getGappedLength() + getInset(getSequenceIndex(source))) ==
+// (longestSequence.getGappedLength() +
+// getInset(getSequenceIndex(longestSequence))))) {
+
+// }
+
+ // fire a further event to signal the length has changed
+ fireAlignmentEvent(new AlignmentEvent
+ (this, getSequenceIndex(source), AlignmentEventType.LENGTH_CHANGE));
+ }
+ }
+} // AbstractSequenceAlignment
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequenceAlignment.java,v $
+ * Revision 1.13 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.12 2001/01/23 17:58:57 lord
+ * Added getSubAlignment( SequenceAlignmentRectangle ) method because I
+ * thought it would be useful.
+ *
+ * Revision 1.11 2000/12/20 17:46:09 jns
+ * o added a method to add a sequence alignment to a sequence
+ * alignment. This code may be too inefficient and may be altered at a
+ * later stage, but the idea is to put in import stuff as well as open.
+ *
+ * Revision 1.10 2000/10/31 15:50:11 lord
+ * Put in some code to check for length changes. Its rather imperfect at
+ * the moment and the event handling is not working well.
+ *
+ * Revision 1.9 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.8 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.7 2000/06/13 11:09:17 lord
+ * Fixed getLength/getGappedLength bug.
+ *
+ * Revision 1.6 2000/03/27 18:47:21 lord
+ * Inserted setLengthQuietly
+ * setInset now checks for length change. Code moved upwards from
+ * DefaultSequenceAlignment.
+ * Changed exception handling
+ *
+ * Revision 1.5 2000/03/20 16:47:21 lord
+ * Moved getInsert upto SequenceAlignment class
+ *
+ * Revision 1.4 2000/03/17 19:40:30 jns
+ * added stuff for insets/preceeding gaps to an sequence within an
+ * alignment.
+ *
+ * Revision 1.4 2000/03/17 18:30:48 jns
+ * added in the concept of inset/preceeding gaps to a sequence
+ * in a sequence alignment.
+ *
+ * Revision 1.3 2000/03/14 16:06:16 lord
+ * Implements VetoableSequenceListener
+ *
+ * Revision 1.2 2000/03/10 17:56:17 lord
+ * Added protected event firing methods
+ * Now also handles most of the sequence event multicasting
+ *
+ * Revision 1.1 2000/03/02 19:21:30 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.java b/src/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.java
new file mode 100644
index 0000000..3f9068a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/AlignmentColumn.java
@@ -0,0 +1,142 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Element;
+
+
+/**
+ * AlignmentColumn.java
+ *
+ * The Sequence and SequenceAlignment classes have been created to be fail-fast. They
+ * throw exceptions if attempts are made to access and element outside
+ * of the range of the sequence. Additionally the alignment allows
+ * sequences to start at any place within the alignment which is very
+ * nice, but has the disadvantage of being a little fiddly to use in some
+ * circumstances. This class addresses this problem. Essentially it is
+ * a mask over a sequence alignment. It can be moved to any column of
+ * the alignment, and will then return the elements down that
+ * column. It takes care of the offsets, and returns a simple gap
+ * Element if a request is made for an Element from before a sequence
+ * starts or after a sequence finishes, so long as the row > 0 and <
+ * alignment.getLength().
+ *
+ * Created: Wed Jun 7 14:23:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentColumn.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentColumn
+{
+
+ private SequenceAlignment alignment;
+ // init this to 1 as it makes more sense that 0.
+ private int column = 1;
+
+ public AlignmentColumn()
+ {
+ }
+
+ public AlignmentColumn( SequenceAlignment alignment )
+ {
+ this();
+ setAlignment( alignment );
+ }
+
+ public void setAlignment( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ }
+
+ public SequenceAlignment getAlignment()
+ {
+ return alignment;
+ }
+
+ public void setColumn( int column )
+ {
+ this.column = column;
+ }
+
+ public int getColumn()
+ {
+ return column;
+ }
+
+ /**
+ * Get the element for this column at the given row. This will
+ * return a Gap element if in front or after the sequence.
+ * @param row the row
+ * @throws NoSuchSequenceException if row < 1 or row > getNumberSequences()
+ * @throws IllegalStateException if the alignment has not been set
+ * @return the element
+ */
+ public Element getElementAtRow( int row ) throws NoSuchSequenceException, IllegalStateException
+ {
+ int alignmentHeight;
+ try{
+ alignmentHeight = alignment.getNumberSequences();
+ }
+ catch( NullPointerException npe ){
+ throw new IllegalStateException( "No alignment given" );
+ }
+
+ // are we in front of the sequence (also throws
+ // NoSuchSequenceException if out of bounds)
+ int inset = alignment.getInset( row );
+ if( column < inset + 1 ){
+ //System.out.println( "Before the start of the gapped sequence " );
+ return Gap.GAP;
+ }
+
+ GappedSequence sequence = alignment.getSequenceAt( row );
+ if( column > sequence.getGappedLength() + inset ){
+ //System.out.println( "Off the end of the gapped sequence therefore gap" );
+ return Gap.GAP;
+ }
+
+ return sequence.getGappedElementAt( column - inset );
+ }
+} // AlignmentColumn
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentColumn.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:18:02 lord
+ * Cosmetic
+ *
+ * Revision 1.1 2000/06/13 11:08:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.java b/src/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.java
new file mode 100644
index 0000000..04fa7c5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/DefaultGappedSequence.java
@@ -0,0 +1,394 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.DefaultSequence;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Residue;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.util.IntArrayList;
+import uk.ac.man.bioinf.sequence.EmptySequence;
+
+
+/**
+ * DefaultGappedSequence.java
+ *
+ *
+ * Created: Sat Mar 4 12:28:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultGappedSequence.java,v 1.14 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultGappedSequence extends AbstractGappedSequence
+{
+ protected Sequence sequence;
+
+ // maps between the gapped and ungapped position. Ive choosen to
+ // just ignore the first element in this list because its not worth
+ // bothering with -1's everywhere. A negative number in this list
+ // means that there is a gap at that point. Ive havent quite decided
+ // what to do with the negative numbers. It might be wise to have it
+ // point to the next non gapped element for instance, although it
+ // might not be worth the computation of doing that. What is clear
+ // however is if its negative its a gap!!!!
+ protected IntArrayList toGappedMap;
+
+ protected DefaultGappedSequence( Sequence seq, IntArrayList toGappedMap )
+ {
+ super( seq.getSequenceType() );
+ this.sequence = seq;
+ this.toGappedMap = toGappedMap;
+ }
+
+ protected DefaultGappedSequence( Element[] elements, SequenceType type,
+ IntArrayList toGappedMap, Identifier ident )
+ {
+ this( new DefaultSequence( elements, type, ident ), toGappedMap );
+ }
+
+ /**
+ * A new gapped sequence, with no gaps in it!
+ * @param elements
+ * @param type
+ * @param bioInt
+ */
+ public DefaultGappedSequence( Element[] elements, SequenceType type, Identifier ident )
+ {
+ this( elements, type, new IntArrayList(), ident );
+
+ // fill the array list up with ints the same as the their
+ // index. We need to add a zero at the first place, so that we
+ // dont have to deal with the - 1 thing....
+ toGappedMap.add( 0, 0 );
+
+ for( int i = 0; i < elements.length ; i++ ){
+ toGappedMap.add( i + 1 );
+ } //end for( i toGappedMap )
+ }
+
+ public DefaultGappedSequence( Element[] elements, SequenceType type )
+ {
+ this( elements, type, new NoIdentifier() );
+ }
+
+ // gap editor methods
+ protected void deleteGapAtQuietly( int index )
+ {
+ checkGappedRange( index );
+ if( getGappedElementAt( index ) != Gap.GAP ){
+ throw new NoGapAtThisPositionException( this, index );
+ }
+
+ toGappedMap.remove( index );
+ }
+
+ protected void insertGapAtQuietly( int index )
+ {
+ checkGappedRangeForInsert( index );
+
+ toGappedMap.add( index, -1 );
+ }
+
+ // gapped accessor methods
+ public Element getGappedElementAt( int index )
+ {
+ try{
+ int unGapIndex = toGappedMap.get( index );
+
+ if( unGapIndex < 0 )
+ return Gap.GAP;
+
+ return sequence.getElementAt( unGapIndex );
+ }
+ catch( ArrayIndexOutOfBoundsException ofbe ){
+ throw getGappedSequenceIndexException( index );
+ }
+ }
+
+ public Element[] getGappedSequenceAsElements()
+ {
+ Element[] elem = new Element[ getGappedLength() ];
+
+ for( int i = 0; i < elem.length; i++ ){
+ elem[ i ] = getGappedElementAt( i + 1 );
+ } //end for( i < elem.length )
+ return elem;
+ }
+
+ public int getGappedLength()
+ {
+ return toGappedMap.size() - 1;
+ }
+
+ public int getUngappedPositionOf( int index )
+ {
+ checkGappedRange( index );
+ return toGappedMap.get( index );
+ }
+
+ public int getGappedPositionOf( int index )
+ {
+ checkRange( index );
+
+ // the gapped index must be greater or equal to the ungapped
+ // index. Therefore start at index in the gap map and work down
+ // till we find it. This could be improved significantly by
+ // making the negative values meaningful. We could also help out
+ // here a lot by doing some sort of binary search
+ for( int i = index; i != getGappedLength(); i++ ){
+ if( toGappedMap.get( i ) == index ){
+ return i;
+ }
+ }
+
+ // If my calculations have not gone awry if we get here there is a
+ // problem with my code!
+ throw new Error( "Failed to find ungapped index which should have been there" );
+ }
+
+ public GappedSequence getGappedSubSequence( int position, int length )
+ {
+ int startUnGap = position;
+ // the end index is the start index, plus the length, which gives
+ // the first element NOT to be included, -1 to give the index of
+ // the last element to be included!
+ int endUnGap = position + length - 1;
+
+ // check the ranges to make sure that everything is correct.
+ checkGappedRange( startUnGap );
+ checkGappedRange( endUnGap );
+
+ // First copy the relevant chunk of the gap map out.
+ IntArrayList newGapMap = toGappedMap.getSubList( position, length );
+
+ // now move all the numbers down..
+ int numberOfGaps = position - getUngappedPositionOf( position );
+ int startPos = position - numberOfGaps;
+
+ for ( int i = 0; i < length; i++ ){
+ int val;
+ if( (val = newGapMap.get(i)) > 0 ) {
+ newGapMap.set( i, val - startPos + 1 );
+ }
+ }
+
+ // We ignore the first element of the IntArrayList in this class
+ // so add a new one on.
+ newGapMap.add( 0, 0 );
+
+
+ // we now need to chomp the begining and the end positions if
+ // there are gaps in the sequence at this point. We move inwards
+ // till we get the first none gap from both ends. The gap model
+ // should still automatically reflect this.
+
+ // search for the first non gap position, going upwards
+ while( getUngappedPositionOf( startUnGap ) == -1 ){
+ startUnGap++;
+ }
+
+ // search for the first non gap position going downwards
+ while( getUngappedPositionOf( endUnGap ) == -1 ){
+ endUnGap--;
+ }
+
+ int interval = endUnGap - startUnGap + 1;
+
+ // if this is less than 1 its all gaps
+ Sequence seq;
+ if( interval < 1 ){
+ seq = EmptySequence.getInstance();
+ }
+ else{
+ // now we need a subsequence for internal use
+ seq =
+ sequence.getSubSequence
+ ( startUnGap - numberOfGaps,
+ interval );
+ }
+
+ // now we can make a new gapped sequence with the private cons
+ return new DefaultGappedSequence( seq, newGapMap );
+ }
+
+ public int getLength()
+ {
+ return sequence.getLength();
+ }
+
+ public Identifier getIdentifier()
+ {
+ return sequence.getIdentifier();
+ }
+
+ public Element[] getSequenceAsElements()
+ {
+ return sequence.getSequenceAsElements();
+ }
+
+ public Element getElementAt( int index )
+ {
+ return sequence.getElementAt( index );
+ }
+
+ public static GappedSequence getElementsAsGappedSequence( Element[] elements, SequenceType type )
+ {
+ return getElementsAsGappedSequence( elements, type, new NoIdentifier() );
+ }
+
+ public static GappedSequence getElementsAsGappedSequence
+ ( Element[] elements, SequenceType type, Identifier ident )
+ {
+
+ // first we need to make a gapped model...
+ IntArrayList gapModel = getGapModelForElements( elements );
+
+ Element[] unGappedElements = stripGapsFromElements
+ ( elements, gapModel.get( 0 ) );
+
+ return new DefaultGappedSequence( unGappedElements, type, gapModel, ident );
+ }
+
+ public static Residue[] stripGapsFromElements( Element[] elements, int size )
+ {
+ Residue[] strippedElements = new Residue[ size ];
+
+ int nonGappedPosition = 0;
+
+ for( int i = 0; i < elements.length; i++ ){
+ if( elements[ i ] != Gap.GAP ){
+ strippedElements[ nonGappedPosition++ ] = (Residue)elements[ i ];
+ }
+ } //end for( i elements.length )
+
+ return strippedElements;
+ }
+
+
+ public static IntArrayList getGapModelForElements( Element[] elements )
+ {
+ // first we need to make a gapped model...
+ IntArrayList gapModel = new IntArrayList( elements.length );
+ // profligately throw away the first element
+ gapModel.add( 0 );
+
+ int nonGappedPosition = 0;
+
+
+ // linear time scan to set up gap model
+ for( int i = 0; i < elements.length; i++ ){
+ if( elements[ i ] == Gap.GAP ){
+ gapModel.add( -1 );
+ }
+ else{
+ gapModel.add( ++nonGappedPosition );
+ }
+ } //end for( i < elements.length )
+
+ // HACK ALERT! HACK ALERT
+ // I need this final value of nonGappedPosition, because it tells
+ // me how many non-Gap elements there are in the Element array,
+ // and I want to use this later. But I have no way of passing this
+ // back from this method. Except that I have a spare place in the
+ // IntArrayList that I am not using. So I'm going to use that to
+ // store this value.
+
+ // This whole classes needs sorting out anyway, with a properly
+ // defined GapModel, rather than this hack, so I am not feeling to
+ // guilty about doing this.
+ gapModel.set( 0, nonGappedPosition );
+
+ return gapModel;
+ }
+
+ public void debugScreenDump()
+ {
+ System.out.println( "Internal sequence is " );
+ Sequences.printSequence( sequence );
+ System.out.println( "Internal gap model is " );
+ toGappedMap.print();
+ }
+
+} // DefaultGappedSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultGappedSequence.java,v $
+ * Revision 1.14 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.13 2001/02/19 17:48:04 lord
+ * Various bug fixes to the subsequence method
+ *
+ * Revision 1.12 2001/01/04 15:07:36 lord
+ * cosmetic
+ *
+ * Revision 1.11 2000/12/13 16:34:58 lord
+ * Alternations to static methods to make gap models accessible for
+ * outside use. This is a temporary hack. The gap model needs re-writing
+ * formally.
+ *
+ * Revision 1.10 2000/11/02 14:56:25 jns
+ * o changed creation of NoGapAt...Exception to store information about
+ * where the exception was raised and by what.
+ *
+ * Revision 1.9 2000/09/11 13:18:13 lord
+ * Added identifier support
+ *
+ * Revision 1.8 2000/07/18 12:37:47 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.7 2000/05/18 17:04:26 lord
+ * Added support for passing in BioObject in cons
+ *
+ * Revision 1.6 2000/03/23 19:51:37 lord
+ * Improved range checking for efficiency of access to elements
+ *
+ * Revision 1.5 2000/03/16 16:14:46 lord
+ * Fixed numerous bugs in getGappedSubsequences
+ *
+ * Revision 1.4 2000/03/14 19:43:43 jns
+ * o sorting problem of translation between gapped and ungapped indicies.
+ *
+ * Revision 1.3 2000/03/14 15:11:34 lord
+ * Inserted static getElementsAsGappedSequence
+ *
+ * Revision 1.2 2000/03/14 13:21:38 lord
+ * Can now add at end
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.java b/src/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.java
new file mode 100644
index 0000000..1b483f0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/DefaultSequenceAlignment.java
@@ -0,0 +1,516 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+
+import java.util.ArrayList;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.InvalidSequenceTypeException;
+import uk.ac.man.bioinf.sequence.NoSuchSequenceElementException;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.util.IntArrayList;
+
+
+/**
+ * DefaultSequenceAlignment.java
+ *
+ * A class to model the multiple sequence alignment.
+ * NB: Sequence numbering starts at 1 <b>NOT</b> 0.
+ *
+ * Created: Mon Feb 21 13:51:11 2000
+ *
+ * @author J Selley
+ * @version $Id: DefaultSequenceAlignment.java,v 1.24 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultSequenceAlignment extends AbstractSequenceAlignment
+{
+ /* (PENDING: JNS) 24.10.00 Change msa from ArrayList to
+ * GappedSequenceArrayList to prevent nasty casting.
+ */
+ // having array list here makes it nasty for casting
+ private ArrayList msa;
+ private Identifier ident;
+ private SequenceType type;
+ private int length;
+ private IntArrayList inset;
+
+ protected void init(GappedSequence[] seqs, SequenceType type,
+ int[] inset, Identifier ident)
+ {
+ // set up msa, inset, type and ident
+ this.msa = new ArrayList();
+ this.inset = new IntArrayList();
+ this.type = type;
+ this.ident = ident;
+
+ // create sequences and put in msa
+ for (int i = 0; i < seqs.length; i++) {
+ this.msa.add(seqs[ i ]);
+ this.inset.add(inset[ i ]);
+ /*
+ * this may be changed later to enable controlled firing of events
+ * ie: so that events are not nedlessly fired until this object
+ * has a listener, at which point this will register with all
+ * sequences and start relaying the events. However, for the meantime
+ * this trivial implementation has been provided because MSAs
+ * will rarely not have a listener
+ */
+ ((GappedSequence)msa.get(i)).addSequenceListener(this);
+ // check the length of the sequence is not the longest
+ if (((GappedSequence)msa.get(i)).getGappedLength() + this.inset.get(i) > this.length)
+ this.length = ((GappedSequence)msa.get(i)).getGappedLength() + this.inset.get(i);
+ }
+ }
+
+ public DefaultSequenceAlignment(SequenceType type)
+ {
+ this.init(new GappedSequence[0], type, new int[0], new NoIdentifier());
+ }
+
+ public DefaultSequenceAlignment(SequenceType type, Identifier ident)
+ {
+ this.init(new GappedSequence[0], type, new int[0], ident);
+ }
+
+ public DefaultSequenceAlignment(Element[][] seqs, SequenceType type)
+ {
+ GappedSequence[] msa = new GappedSequence[seqs.length];
+
+ // create sequences and put in msa
+ for (int i = 0; i < seqs.length; i++) {
+ msa[i] = new DefaultGappedSequence(seqs[i], type);
+ /*
+ * this may be changed later to enable controlled firing of events
+ * ie: so that events are not nedlessly fired until this object
+ * has a listener, at which point this will register with all
+ * sequences and start relaying the events. However, for the meantime
+ * this trivial implementation has been provided because MSAs
+ * will rarely not have a listener
+ */
+ msa[i].addSequenceListener(this);
+ }
+
+ // create inset arry to correspond to sequences
+ this.init(msa, type, new int[msa.length], new NoIdentifier());
+ }
+
+ public DefaultSequenceAlignment( GappedSequence[] seqs, SequenceType type,
+ int[] inset, Identifier ident )
+ {
+ this.init(seqs, type, inset, ident);
+ }
+
+
+ public DefaultSequenceAlignment( GappedSequence[] seqs, SequenceType type, int[] inset )
+ {
+ this.init(seqs, type, inset, new NoIdentifier());
+ }
+
+ public DefaultSequenceAlignment(GappedSequence[] seqs, SequenceType type)
+ {
+ this.init(seqs, type, new int[seqs.length], new NoIdentifier());
+ }
+
+ public DefaultSequenceAlignment
+ (SequenceAlignment msa, SequenceType type)
+ {
+ GappedSequence[] seqs = new GappedSequence[msa.getNumberSequences()];
+ int[] inset = new int[msa.getNumberSequences()];
+
+ // iterate through the sequences in msa to copy
+ for (int i = 0; i < msa.getNumberSequences(); i++) {
+ seqs[i] = Sequences.getElementsAsGappedSequence
+ ((msa.getSequenceAt(i)).getGappedSequenceAsElements(), type);
+ inset[i] = msa.getInset(i);
+ /*
+ * this may be changed later to enable controlled firing of events
+ * ie: so that events are not nedlessly fired until this object
+ * has a listener, at which point this will register with all
+ * sequences and start relaying the events. However, for the meantime
+ * this trivial implementation has been provided because MSAs
+ * will rarely not have a listener
+ */
+ seqs[i].addSequenceListener(this);
+ }
+
+ this.init(seqs, type, inset, new NoIdentifier());
+ }
+
+ /**
+ * Returns a sub-alignment, given the exact location in this alignment.
+ * NB: Sequencing numbering and alignment numbering start at 1 <b>NOT</b>
+ * 0.
+ *
+ * @param startPos the start position for the sub-alignment (i.e: x1)
+ * @param length the length of the sub-alignment
+ * @param startSeq the first sequence in the current alignment to be
+ * included in the sub-alignment (i.e: y1)
+ * @param numSeqs the number of sequences to be included in the
+ * sub-alignment
+ * @return the sub-MSA
+ */
+ public SequenceAlignment getSubAlignment(int startPos, int length,
+ int startSeq, int numSeqs)
+ {
+ // check all params are "logical"
+ // NB: all numbering starts at 1 NOT 0
+ if (startPos < 1)
+ throw new NoSuchSequenceElementException
+ ("Attempt to access element at zero or negative index. Sequences start " +
+ "at index 1");
+ if ( (startPos + length) > getLength() )
+ throw new NoSuchSequenceElementException
+ ("Attempt to access element greater than sequence alignment length");
+ if (startSeq < 1)
+ throw new NoSuchSequenceException
+ ("Attempt to access a sequence at zero or negative index. Indexing " +
+ "starts at 1");
+ if (((startSeq - 1) + numSeqs) > msa.size())
+ throw new NoSuchSequenceException
+ ("Attempt to access a sequence with an index greater than the " +
+ "alignment length");
+
+ // define the sub-alignment
+ GappedSequence[] sequences = new GappedSequence[ numSeqs ];
+ int[] insets = new int[ numSeqs ];
+
+ int index = 0;
+
+ // ...and cycle through entering each sub-sequence into alignment
+ for ( int i = startSeq; i < ( startSeq + numSeqs ); i++ ) {
+ // there are several different possibilities that we need to
+ // cover here. The first of these is that the GappedSequence
+ // either finishes before the start of this subsequence, or
+ // starts after it.
+
+ // starts after it...
+ if( getInset( i ) > ( startPos + length ) ||
+ // ends before it
+ ( getInset( i ) + getSequenceAt( i ).getLength() ) < startPos ){
+
+ insets[ index ] = startPos + length;
+ sequences[ index++ ] = EmptyGappedSequence.getInstance();
+ }
+ else{
+ // calculate distance to start of sequence
+ insets[ index ] = getInset( i ) - startPos + 1;
+ // we only want this distance if its positive, otherwise there
+ // is not inset.
+ insets[ index ] = Math.max( insets[ index ], 0 );
+
+
+
+ // calculate the start position. This is 1 minimum (if we are
+ // starting before the sequence starts) or the startPosition
+ // in the alignment minus the inset.
+ int beginingSubSeq = Math.max( 1, startPos - getInset( i ) );
+
+ // work out the length that we want to cut
+ int subSeqLength = Math.min
+ // this one deals with the situation when we are going of
+ // the end of the sequence.
+ ( (getSequenceAt( i ).getLength() - beginingSubSeq + 1),
+ // and this one deals with the situation where we are not.
+ (length - insets[ index ] ) );
+
+ // fetch the new sub sequence
+ sequences[ index++ ] =
+ getSequenceAt( i ).getGappedSubSequence( beginingSubSeq, subSeqLength );
+ }
+ }
+
+ // return a new instance of DefaultSequenceAlignment
+ return new DefaultSequenceAlignment( sequences, this.type, insets );
+ }
+
+ /**
+ * Returns the sequence type for the alignment (e.g: Protien Sequence).
+ *
+ * @return the sequence type
+ */
+ public SequenceType getSequenceType()
+ {
+ return this.type;
+ }
+
+ /**
+ * Returns the sequence, given a specific location in the MSA.
+ * NB: Alignment sequence numbering begins at 1 <b>NOT</b> 0.
+ *
+ * @param index the location in the MSA of the target sequence
+ * @return the sequence
+ */
+ public GappedSequence getSequenceAt(int index)
+ {
+ try{
+ // remember sequence numbering in an alignment begins at 1 NOT 0
+ return (GappedSequence)this.msa.get(index - 1);
+ }
+ catch( IndexOutOfBoundsException aie ){
+ // throw and exception of the right type
+ throw new NoSuchSequenceException( "The index " + index + " is out of bounds", this, index );
+ }
+ }
+
+ /**
+ * Returns the location of a sequence, in the multiple sequence alignment.
+ * NB:
+ *
+ * @param seq the sequence of interest
+ * @return the location (-1 if sequence not found)
+ */
+ public int getSequenceIndex(GappedSequence seq)
+ {
+ // iterate through msa and return i if sequence found
+ for (int i = 0; i < msa.size(); i++) {
+ if ((GappedSequence)msa.get(i) == seq)
+ // sequence numbering starts at 1 NOT 0
+ return i + 1;
+ }
+
+ // else return -1
+ return -1;
+ }
+
+ protected void setLengthQuietly( int length )
+ {
+ this.length = length;
+ }
+
+ /**
+ * Adds a sequence quietly to the alignment (i.e., without notifying
+ * listeners - it should really only be done from it's parent
+ * procedure addSequence).
+ *
+ * @param seq the sequence
+ * @param inset the sequence inset in the alignment
+ */
+ protected void addSequenceQuietly(GappedSequence seq, int inset)
+ {
+ if( seq.getSequenceType() != type )
+ throw new InvalidSequenceTypeException
+ ( "All sequences must be of the same type" );
+
+ // add this object as a listener of the sequence
+ seq.addSequenceListener(this);
+
+ // add the sequence and its inset to the alignment
+ this.msa.add(seq);
+ this.inset.add(inset);
+ }
+
+ /**
+ * Removes a sequence from the alignment, quietly, i.e., without
+ * notifying any listeners. This procedure ought only to be called
+ * from its "parent", removeSequence (unless you really know what
+ * you are doing - hence the public nature of the function).
+ * @param seqIndex the sequence index
+ * @return the removed sequence
+ */
+ protected GappedSequence removeSequenceQuietly(int seqIndex)
+ {
+ GappedSequence removedSequence = null;
+
+ try {
+ // N.B.: sequence indexing starts at 1 NOT 0
+ // remove the sequence from the msa and store
+ removedSequence = (GappedSequence)msa. remove(seqIndex - 1);
+ // remove the associated inset
+ inset.remove(seqIndex - 1);
+
+ // remove ourself as a listener of the sequence
+ removedSequence.removeSequenceListener(this);
+ } catch (IndexOutOfBoundsException e) {
+ throw new NoSuchSequenceException(this, seqIndex);
+ }
+
+ // return the sequence removed - will be null if couldn't find
+ return removedSequence;
+ }
+
+ /**
+ * Sets the inset (or preceeding number of gaps) for a sequence in the
+ * alignment.
+ *
+ * @param seqIndex the sequence index for the inset to be added to
+ * @param inset the inset
+ */
+ protected void setInsetQuietly(int seqIndex, int inset)
+ {
+ try{
+ // NB: seqIndex runs from 1 NOT 0
+ this.inset.set(seqIndex - 1, inset);
+ }
+ catch( ArrayIndexOutOfBoundsException aie ){
+ throw new NoSuchSequenceException(this, seqIndex);
+ }
+ }
+
+ /**
+ * Returns the inset of a particular sequence in the alignment.
+ *
+ * @param seqIndex the sequence index
+ * @return the inset
+ */
+ public int getInset(int seqIndex)
+ {
+ try{
+ // NB: seqIndex starts at 1 NOT 0
+ return this.inset.get(seqIndex - 1);
+ }
+ catch( ArrayIndexOutOfBoundsException aie ){
+ throw new NoSuchSequenceException(this, seqIndex);
+ }
+ }
+
+ /**
+ * Returns the total number of sequences in the multiple sequence alignment.
+ *
+ * @return the total number of sequences
+ */
+ public int getNumberSequences()
+ {
+ return msa.size();
+ }
+
+ /**
+ * Returns the length of the multiple sequence alignment.
+ *
+ * @return the length
+ */
+ public int getLength()
+ {
+ return this.length;
+ }
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+} // DefaultSequenceAlignment
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultSequenceAlignment.java,v $
+ * Revision 1.24 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.23 2001/01/19 19:49:11 lord
+ * Fixed bug in exception handling
+ *
+ * Revision 1.22 2001/01/04 15:08:49 lord
+ * getSubAlignment now copes correctly with insets.
+ *
+ * Revision 1.21 2000/10/31 15:49:41 lord
+ * Tightened access on some methods which bypass the event system
+ *
+ * Revision 1.20 2000/10/26 18:54:18 lord
+ * setInsetQuietly methods to be protected
+ *
+ * Revision 1.19 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.18 2000/09/22 14:31:00 jns
+ * o bug fixing: the length of the alignment did not take into account
+ * the insets. This has now been fixed by setting an init function which
+ * all constructors have to and will have to call. Not elegant, but it
+ * works.
+ *
+ * Revision 1.17 2000/09/11 13:18:13 lord
+ * Added identifier support
+ *
+ * Revision 1.16 2000/06/13 11:08:12 lord
+ * Fixed getLength/getGappedLength bug.
+ * Exception Handling now fulfils the interface requirements
+ *
+ * Revision 1.15 2000/06/05 14:24:29 lord
+ * Cosmetic changes
+ *
+ * Revision 1.14 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.13 2000/05/18 17:04:00 lord
+ * No longer clones all of the Sequences that it is given in the cons.
+ * Added support for passing insets into cons
+ *
+ * Revision 1.12 2000/03/27 18:48:12 lord
+ * Removed length increase handling upwards.
+ * Added setLengthQuietly method
+ *
+ * Revision 1.11 2000/03/21 18:22:33 lord
+ * Fixed bug in setInsetQuiety. Now increases alignment length if necessary
+ *
+ * Revision 1.10 2000/03/21 14:33:14 jns
+ * o corrected my ****-up, and sorted this class so it compiles.
+ *
+ * Revision 1.9 2000/03/21 13:13:03 jns
+ * adding index checking to setInset and getInset.
+ *
+ * Revision 1.8 2000/03/20 16:08:40 jns
+ * o setting ability to deal with insets.
+ *
+ * Revision 1.7 2000/03/14 19:44:25 jns
+ * o debugging
+ * o sorting problem of translation between gapped and ungapped indicies.
+ *
+ * Revision 1.6 2000/03/14 16:53:43 jns
+ * o messed up on getSubAlignment... corrected.
+ *
+ * Revision 1.5 2000/03/14 16:42:41 jns
+ * o changed getSubAlignment to use Sequences static class.
+ *
+ * Revision 1.4 2000/03/14 16:34:22 jns
+ * o changed getSubAlignment to deal with length and numSeqs rather than endSeq
+ * and endPos.
+ * o added sequence listener support to register with all sequences as added to
+ * the aligment in the constructors. This may be changed at a later date to
+ * prevent the firing of events when there are no listeners to this object. This
+ * would work by only registering with each sequence when a listener registers
+ * with this object. The reason for not immediately implementing this is that
+ * it is assumed that normally an alignment will have listeners.
+ *
+ * Revision 1.3 2000/03/14 16:13:46 jns
+ * added use of Sequences static class.
+ *
+ * Revision 1.2 2000/03/10 17:55:15 lord
+ * Moved all of the listener handling to super class
+ *
+ * Revision 1.1 2000/03/10 12:11:19 jns
+ * initial code.
+ *
+ */
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.java b/src/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.java
new file mode 100644
index 0000000..81f9b2c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/EmptyGappedSequence.java
@@ -0,0 +1,202 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.NoSuchSequenceElementException;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.NoGapAtThisPositionException;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.types.EmptySequenceType;
+
+
+/**
+ * EmptyGappedSequence.java
+ *
+ *
+ * Created: Tue Nov 7 18:15:06 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: EmptyGappedSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class EmptyGappedSequence implements GappedSequence
+{
+ private static final EmptyGappedSequence instance = new EmptyGappedSequence();
+
+ public static EmptyGappedSequence getInstance()
+ {
+ return instance;
+ }
+
+ private EmptyGappedSequence()
+ {
+ }
+
+ private NoSuchSequenceElementException createException()
+ {
+ return new NoSuchSequenceElementException
+ ( "Empty Gapped Sequence does not do much" );
+ }
+
+ // implementation of uk.ac.man.bioinf.sequence.Sequence interface
+ public Sequence getSubSequence(int param1, int param2)
+ {
+ if( param1 != 0 || param2 != 0 )
+ throw createException();
+
+ return this;
+ }
+
+ public SequenceType getSequenceType() {
+ return EmptySequenceType.getInstance();
+ }
+
+ private static Element[] noElements = new Element[ 0 ];
+ public Element[] getSequenceAsElements() {
+ return noElements;
+ }
+
+ private static char[] noChars = new char[ 0 ];
+
+ public char[] getSequenceAsChars() {
+ return noChars;
+ }
+
+ public int getLength() {
+ return 0;
+ }
+
+ public char getElementAtAsChar(int param1) {
+ throw createException();
+ }
+
+ public Element getElementAt(int param1) {
+ throw createException();
+ }
+
+ public void insertGapAt(int param1, int param2) throws NoSuchSequenceElementException, SequenceVetoException {
+ throw createException();
+ }
+
+
+ public void insertGapAt(int param1) throws NoSuchSequenceElementException, SequenceVetoException {
+ throw createException();
+ }
+
+ public int getUngappedPositionOf(int param1) {
+ throw createException();
+ }
+
+ public GappedSequence getGappedSubSequence(int param1, int param2) {
+ if( param1 != 0 || param2 != 0 )
+ throw createException();
+ return this;
+ }
+
+ public Element[] getGappedSequenceAsElements() {
+ return noElements;
+ }
+
+ public char[] getGappedSequenceAsChars() {
+ return noChars;
+ }
+
+
+ public int getGappedPositionOf(int param1) {
+ throw createException();
+ }
+
+ public int getGappedLength() {
+ return 0;
+ }
+
+ public char getGappedElementAtAsChar(int param1) {
+ throw createException();
+ }
+
+ public Element getGappedElementAt(int param1) {
+ throw createException();
+ }
+
+ public void deleteGapAt(int param1, int param2)
+ throws NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException {
+ throw createException();
+ }
+
+ public void deleteGapAt(int param1)
+ throws NoGapAtThisPositionException, NoSuchSequenceElementException, SequenceVetoException {
+ throw createException();
+ }
+ // implementation of uk.ac.man.bioinf.sequence.identifier.Identifiable interface
+ // this is immutable so we can use a shared instance.
+ private static Identifier ident = new NoIdentifier();
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+
+ public void removeVetoableSequenceListener(VetoableSequenceListener param1) {
+ // do nothing here!
+ }
+
+ public void removeSequenceListener(SequenceListener param1) {
+ // do nothing
+ }
+
+ public void addVetoableSequenceListener(VetoableSequenceListener param1) {
+ // do nothing
+ }
+
+ public void addSequenceListener(SequenceListener param1) {
+ // do nothing
+ }
+} // EmptyGappedSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: EmptyGappedSequence.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/11/08 18:20:36 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.java b/src/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.java
new file mode 100644
index 0000000..3ba1bfe
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/EmptySequenceAlignment.java
@@ -0,0 +1,234 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.types.EmptySequenceType;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+
+
+/**
+ * EmptySequenceAlignment.java
+ *
+ *
+ * Created: Wed Apr 19 17:23:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: EmptySequenceAlignment.java,v 1.7 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class EmptySequenceAlignment implements SequenceAlignment
+{
+ private static final EmptySequenceAlignment instance = new EmptySequenceAlignment();
+
+ public static EmptySequenceAlignment getInstance()
+ {
+ return instance;
+ }
+
+ private EmptySequenceAlignment()
+ {
+ }
+
+ private NoSuchSequenceException createSequenceException( int index )
+ {
+ return new NoSuchSequenceException
+ ( "Empty sequence does not do much", this, index );
+ }
+
+ public int getInset( int index )
+ {
+ throw createSequenceException( index );
+ }
+
+ public int getLength()
+ {
+ return 0;
+ }
+
+ public int getNumberSequences()
+ {
+ return 0;
+ }
+
+ public GappedSequence getSequenceAt( int index )
+ {
+ throw createSequenceException( index );
+ }
+
+ public int getSequenceIndex( GappedSequence seq )
+ {
+ return -1;
+ }
+ //setModel( new SequenceAlignmentBoundRangeModelBridge( seq ) );
+ public SequenceType getSequenceType()
+ {
+ return EmptySequenceType.getInstance();
+ }
+
+ public SequenceAlignment getSubAlignment( int a, int b, int c, int d )
+ {
+ if( a != 0 || b != 0 || c != 0 || d != 0 )
+ throw createSequenceException( a );
+
+ else return this;
+ }
+
+ public SequenceAlignment getSubAlignment( SequenceAlignmentRectangle rect )
+ {
+ return getSubAlignment( rect.getX(), rect.getWidth(), rect.getY(), rect.getHeight() );
+ }
+
+ public void setInset(int seqIndex, int size)
+ {
+ // no implementation necessary
+ }
+
+ public void setInsetQuietly( int seqIndex, int inset )
+ {
+ // no implementation necessary
+ }
+
+ public void addSequence(GappedSequence seq, int inset)
+ {
+ // no implementation necessary
+ }
+
+ public GappedSequence removeSequence(int seqIndex)
+ {
+ throw createSequenceException(seqIndex);
+ }
+
+ public void setLengthQuietly( int length )
+ {
+ // no implementation necessary
+ }
+
+ // we need no implementation here. There is only one instance and it
+ // has a static reference to it. As this alignment can not change
+ // there is no point keeping references to it. Worse still if we do
+ // keep references it will keep the entire listener from GC'ing at
+ // any point.
+ public void addAlignmentListener(AlignmentListener listener)
+ {
+ }
+
+ public void removeAlignmentListener(AlignmentListener listener)
+ {
+ }
+
+ public void addVetoableAlignmentListener(VetoableAlignmentListener listener)
+ {
+ }
+
+ public void removeVetoableAlignmentListener(VetoableAlignmentListener listener)
+ {
+ }
+
+ public void vetoableChangeOccurred( VetoableSequenceEvent event )
+ {
+ }
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ }
+
+ public void addSequenceListener( SequenceListener listener )
+ {
+ }
+
+ public void addVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ }
+
+ public void removeSequenceListener( SequenceListener listener )
+ {
+ }
+
+ public void removeVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ }
+
+ // this is immutable so we can use a shared instance.
+ private static Identifier ident = new NoIdentifier();
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+} // EmptySequenceAlignment
+
+
+
+/*
+ * ChangeLog
+ * $Log: EmptySequenceAlignment.java,v $
+ * Revision 1.7 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.6 2001/01/23 17:58:57 lord
+ * Added getSubAlignment( SequenceAlignmentRectangle ) method because I
+ * thought it would be useful.
+ *
+ * Revision 1.5 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.4 2000/09/15 17:24:01 lord
+ * This class has a very nasty bug in it. It was extending from
+ * AbstractSequenceAlignment. Which meant it was storing listeners that
+ * were adding to it. The problem was that the instance has a static
+ * reference to it (as it stored as a singleton). This was causing a bad
+ * memory leak in my code, which took me two days to find.
+ *
+ * The irony is that I only extended from AbstractSequenceAlignment
+ * because I wrote the code on a friday night and was being lazy, and I
+ * only used the singleton because for reasons of efficiency. Combining
+ * an optimisation and friday night code naturally produced an appalling
+ * bug.
+ *
+ * Revision 1.3 2000/09/11 13:18:13 lord
+ * Added identifier support
+ *
+ * Revision 1.2 2000/08/01 17:16:20 lord
+ * Now returns EmptySequenceType rather than null
+ *
+ * Revision 1.1 2000/04/20 14:40:16 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/Gap.java b/src/uk/ac/man/bioinf/sequence/alignment/Gap.java
new file mode 100644
index 0000000..5137ee5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/Gap.java
@@ -0,0 +1,85 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Element;
+
+
+/**
+ * Gap.java
+ *
+ *
+ * Created: Wed Mar 1 19:35:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Gap.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class Gap implements Element
+{
+ private Gap()
+ {}
+
+ public char toChar()
+ {
+ return '-';
+ }
+
+ public String toString()
+ {
+ return "Gap Element";
+ }
+
+
+ public static final Gap gap = new Gap();
+ public static final Gap GAP = gap;
+} // Gap
+
+
+
+/*
+ * ChangeLog
+ * $Log: Gap.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/08/21 16:12:17 jns
+ * o removing toURL and toResourceString, which were part of the BioInterface
+ * stuff that was removed about a month ago.
+ *
+ * Revision 1.2 2000/03/08 17:24:33 lord
+ * *** empty log message ***
+ *
+ * Revision 1.1 2000/03/01 20:17:14 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/GappedSequence.java b/src/uk/ac/man/bioinf/sequence/alignment/GappedSequence.java
new file mode 100644
index 0000000..6b76c1b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/GappedSequence.java
@@ -0,0 +1,148 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.MutableSequence;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.NoSuchSequenceElementException;
+
+/**
+ * GappedSequence.java
+ *
+ *
+ * Created: Wed Mar 1 18:28:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GappedSequence.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface GappedSequence extends MutableSequence
+{
+ public GappedSequence getGappedSubSequence( int from, int length );
+
+ public Element getGappedElementAt( int position );
+
+ public char getGappedElementAtAsChar( int position );
+
+ public Element[] getGappedSequenceAsElements();
+
+ public char[] getGappedSequenceAsChars();
+
+ /**
+ * Returns the gapped length of this sequence. That is the length of
+ * the sequence including its gaps. Conversely this means that the
+ * getLength method of the Sequence interface returns the length of
+ * the sequence ignoring the gaps.
+ * @return the length
+ */
+ public int getGappedLength();
+
+ /**
+ * Translate between the gapped index, and the ungapped index
+ * @param index the ungapped position
+ * @return the gapped position of the equivalent element
+ */
+ public int getGappedPositionOf( int index );
+
+ /**
+ * Translate between the gapped position and the ungapped
+ * position. I havent quite decided what to do at the moment if the
+ * index refers to a gap. One idea is to throw a
+ * NoSuchSequenceElementException which makes a certain amount of
+ * sense but isnt really that useful. Perhaps a better idea is to
+ * run -(insertion-point) where the insertion point is the nearest
+ * element before the current requested position which is not a
+ * gap. That way a value less than 0 would indicate a gap and would
+ * also return a useful value
+ * @param index
+ * @return
+ */
+ public int getUngappedPositionOf( int index );
+
+ public void insertGapAt( int index ) throws NoSuchSequenceElementException, SequenceVetoException;
+
+ /**
+ * Inserts the elements at this position. If the index is one longer
+ * than the length of the sequence the sequence will be extended.
+ * @param element the elements to insert
+ * @param index the index at which to insert
+ * @throws NoSuchSequenceElementException if the element does not
+ * exist, which will be the case if index is less than 1 or greater
+ * than sequence length + 1
+ */
+ public void insertGapAt( int index, int length ) throws NoSuchSequenceElementException, SequenceVetoException;
+
+ /**
+ * Delete the element at index.
+ * @param index the index to delete
+ * @return the element which has just been deleted
+ * @exception NoSuchSequenceElementException if index is less than 1
+ * or greater than the length of the sequence
+ */
+ public void deleteGapAt( int index ) throws NoGapAtThisPositionException, NoSuchSequenceElementException,
+ SequenceVetoException;
+
+ /**
+ * Delete the elements starting at index for the specified length
+ * @param index the index to start at
+ * @param length the length to delete
+ * @return the elements just deleted
+ * @throws NoSuchSequenceElementException if the elements do not all
+ * exist, so if index is less than 1, or index + length is greater
+ * than the length of the sequence
+ */
+ public void deleteGapAt( int index, int length ) throws NoGapAtThisPositionException,
+ NoSuchSequenceElementException, SequenceVetoException;
+
+}// GappedSequence
+
+
+/*
+ * ChangeLog
+ * $Log: GappedSequence.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2001/01/04 15:05:51 lord
+ * Changed getGappedSubAlignment to start, length, rather than start, stop.
+ *
+ * Revision 1.3 2000/06/13 11:07:12 lord
+ * Improved documentation
+ *
+ * Revision 1.2 2000/03/08 17:24:34 lord
+ * *** empty log message ***
+ *
+ * Revision 1.1 2000/03/01 20:17:14 lord
+ * Initial checkin
+ *
+ * Revision 1.1 2000/03/01 20:14:06 lord
+ * Initial revision
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.java b/src/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.java
new file mode 100644
index 0000000..17bfb75
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/NoGapAtThisPositionException.java
@@ -0,0 +1,99 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+
+
+/**
+ * NoGapAtThisPositionException.java
+ *
+ *
+ * Created: Sat Mar 4 14:04:07 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NoGapAtThisPositionException.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NoGapAtThisPositionException extends RuntimeException
+{
+ private GappedSequence source;
+ private int index;
+
+ public NoGapAtThisPositionException( String message )
+ {
+ super( message );
+ }
+
+ /**
+ * Creates an object signalling an exception for no gap at a
+ * particular position. This constructor stores the source and index
+ * within the source where the exception was raised.
+ * @param message the message to use
+ * @param source the gapped sequence or source
+ * @param index the index in the source of the raised
+ */
+ public NoGapAtThisPositionException(String message, GappedSequence source, int index)
+ {
+ super(message);
+ this.source = source;
+ this.index = index;
+ }
+
+ public NoGapAtThisPositionException(GappedSequence source, int index)
+ {
+ this("No gap was found at " + index + " in sequence " + source,
+ source, index);
+ }
+
+ public GappedSequence getSource()
+ {
+ return this.source;
+ }
+
+ public int getIndex()
+ {
+ return this.index;
+ }
+} // NoGapAtThisPositionException
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoGapAtThisPositionException.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/02 14:56:37 jns
+ * o changed creation of NoGapAt...Exception to store information about
+ * where the exception was raised and by what.
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.java b/src/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.java
new file mode 100644
index 0000000..28d7fd2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/NoSuchSequenceException.java
@@ -0,0 +1,77 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+
+
+/**
+ * NoSuchSequenceException.java
+ *
+ * Alerts to an invalid sequence index within a sequence alignment.
+ *
+ * Created: Fri Mar 3 12:22:15 2000
+ *
+ * @author Julian Selley
+ * @version $Id: NoSuchSequenceException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NoSuchSequenceException extends RuntimeException
+{
+ public NoSuchSequenceException()
+ {
+ super();
+ }
+
+ public NoSuchSequenceException( String message )
+ {
+ super( message );
+ }
+
+ public NoSuchSequenceException( SequenceAlignment msa, int index )
+ {
+ super( "Attempt to access sequence " + index + " of alignment " + msa + " which does not exist" );
+ }
+
+ public NoSuchSequenceException( String message, SequenceAlignment msa, int index )
+ {
+ super( message + ": " + msa + " at " + index );
+ }
+} // NoSuchSequenceException
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoSuchSequenceException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/10 12:11:44 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.java b/src/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.java
new file mode 100644
index 0000000..118c071
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/SequenceAlignment.java
@@ -0,0 +1,227 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.event.SequenceEventProvider;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.identifier.Identifiable;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+
+
+/**
+ * SequenceAlignment.java
+ *
+ * This interface is designed to mimic a biological sequence alignment.
+ * As a consequence, the sequences contained within should be
+ * GappedSequence.
+ * @see GappedSequence
+ *
+ *
+ * Created: Tue Feb 15 16:24:23 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceAlignment.java,v 1.17 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceAlignment extends SequenceEventProvider,
+ VetoableSequenceListener,
+ AlignmentEventProvider,
+ Identifiable
+{
+
+ /**
+ * Returns a sub-alignment, given the exact location in this alignment.
+ *
+ * @param startPos the start position for the sub-alignment (i.e: x1)
+ * @param length the length of the sub alignment
+ * @param startSeq the first sequence in the current alignment to be
+ * included in the sub-alignment (i.e: y1)
+ * @param numSeq the number of sequences to be returned
+ * @return the sub-alignment
+ */
+ public SequenceAlignment getSubAlignment(int startPos, int length,
+ int startSeq, int numSeqs);
+
+ public SequenceAlignment getSubAlignment( SequenceAlignmentRectangle rect );
+
+ /**
+ * Adds a sequence to the current alignment. If listeners are
+ * listening to the alignment, they will be able to veto the add
+ * (thats the idea atleast).
+ *
+ * @param seq the sequence to be added
+ * @param inset the sequence inset
+ * @exception veto to the addition
+ */
+ public void addSequence(GappedSequence seq, int inset)
+ throws AlignmentVetoException;
+
+ /**
+ * Removes a sequence from the alignment. It requires the knowledge
+ * of the sequence location in the alignment.
+ *
+ * @param seqIndex the index of the sequence
+ * @return the sequence
+ * @exception veto to the removal
+ */
+ public GappedSequence removeSequence(int seqIndex)
+ throws AlignmentVetoException;
+
+ /**
+ * Sets the inset of a sequence within the alignment. An inset of
+ * zero will mean that the first element starts at the left most
+ * position of the alignment.
+ * <p>
+ * Special N.B.: This was put into the interface because it was
+ * felt that there would not be any instances when you would not
+ * wish to do this (apart from a read-only alignment, in which case
+ * there are ways and means).
+ * @param seqIndex the index of the sequence
+ * @param size the size of the inset
+ * @exception veto to setting
+ */
+ public void setInset(int seqIndex, int size) throws AlignmentVetoException;
+
+ /**
+ * Returns the inset of sequence within the alignment.
+ * A inset of 0 means that the first element means that the Sequence
+ * starts at the left most position of the alignment
+ * @param seqIndex the sequence index
+ * @return the inset or preceeding number of gaps
+ */
+ public int getInset(int seqIndex);
+
+ /**
+ * Returns the sequence type of the alignment (e.g: protein sequences).
+ *
+ * @return the sequence type
+ */
+ public SequenceType getSequenceType();
+
+ /**
+ * Provides the sequence at a particular location in the alignment.
+ * The indexing STARTS AT 1, and not 0.
+ * @param index the index of the target sequence
+ * @return the sequence of interest
+ * @throws if index < 1 or index > getNumberSequences()
+ */
+ public GappedSequence getSequenceAt(int index) throws NoSuchSequenceException;
+
+ /**
+ * Returns the index in the alignment of a provided sequence.
+ *
+ * @param seq the query sequence
+ * @return the index of the sequence, or -1 if not found
+ */
+ public int getSequenceIndex(GappedSequence seq);
+
+ /**
+ * Returns the total number of sequences in the alignment.
+ *
+ * @return the number of sequences
+ */
+ public int getNumberSequences();
+
+ /**
+ * Returns the length of the alignment (i.e: the longest sequence).
+ *
+ * @return length of alignment
+ */
+ public int getLength();
+
+} // SequenceAlignment
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignment.java,v $
+ * Revision 1.17 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.16 2001/01/23 17:58:57 lord
+ * Added getSubAlignment( SequenceAlignmentRectangle ) method because I
+ * thought it would be useful.
+ *
+ * Revision 1.15 2001/01/04 15:05:11 lord
+ * getSubAlignment method differed from that of getSubAlignment in
+ * DefaultSequenceAlignment (it used start, stop rather than start,
+ * length). It was easier to change the interface, rather than the
+ * implementation.
+ *
+ * Revision 1.14 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.13 2000/11/27 18:17:52 lord
+ * Have removed Identifier methods, now extends Identifiable
+ *
+ * Revision 1.12 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.11 2000/09/11 13:18:13 lord
+ * Added identifier support
+ *
+ * Revision 1.10 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.9 2000/06/13 11:07:00 lord
+ * Improved documentation
+ *
+ * Revision 1.8 2000/06/05 14:45:58 lord
+ * Made documentation more explicit
+ *
+ * Revision 1.7 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.6 2000/05/08 17:06:43 lord
+ * Event methods now removed to secondary interface
+ *
+ * Revision 1.5 2000/04/19 17:15:17 lord
+ * Removed extraneous abstract
+ *
+ * Revision 1.4 2000/03/20 16:47:21 lord
+ * Moved getInsert upto SequenceAlignment class
+ *
+ * Revision 1.3 2000/03/10 17:54:18 lord
+ * Now implements SequenceEventProvider
+ *
+ * Revision 1.2 2000/03/10 12:34:01 jns
+ * unknown changes.
+ * Sequence -> Gapped Sequence I think.
+ *
+ * Revision 1.1 2000/03/02 19:21:52 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.java b/src/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.java
new file mode 100644
index 0000000..c100023
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/SingleSequenceAlignment.java
@@ -0,0 +1,96 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventProvider;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceEventProvider;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+
+
+/**
+ * SingleSequenceAlignment.java
+ *
+ * This class is for those stick occasions when you want a
+ * SequenceAlignment but all you have is a Sequence. I don't know how
+ * to make an array all within a single line so I have had to make a
+ * factory method here.
+ *
+ * Created: Tue Aug 1 16:16:33 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SingleSequenceAlignment.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SingleSequenceAlignment extends DefaultSequenceAlignment
+{
+ public SingleSequenceAlignment( GappedSequence seq )
+ {
+ super( new GappedSequence[]{ seq },seq.getSequenceType() );
+ }
+
+ public int getNumberOfSequences()
+ {
+ return 1;
+ }
+
+ public GappedSequence getSingleSequence()
+ {
+ return getSequenceAt( 1 );
+ }
+} // SingleSequenceAlignment
+
+
+
+/*
+ * ChangeLog
+ * $Log: SingleSequenceAlignment.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/08/01 17:39:13 lord
+ * Worked out how to create an array in one line
+ *
+ * Revision 1.1 2000/08/01 17:17:23 lord
+ * Intial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.java b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.java
new file mode 100644
index 0000000..7a84d43
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEvent.java
@@ -0,0 +1,130 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+import java.util.EventObject;
+
+
+/**
+ * AlignmentEvent.java
+ *
+ * Instances of this class represent an event to a MSA. It includes
+ * reference to the location of the event, as well as its type.
+ *
+ * Created: Tue Feb 15 19:57:49 2000
+ *
+ * @author J Selley
+ * @version $Id: AlignmentEvent.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentEvent extends EventObject
+{
+
+ private int start; // the start location of the event
+ private int end; // the end location of the even
+ private AlignmentEventType type; // the type of event (an enum model)
+
+ /**
+ * Constructor to set the event source, location and type.
+ *
+ * @param src the source of the event (i.e: the MSA)
+ * @param location the location of the event, or zero if not known
+ * @param type the multiple sequence event type
+ */
+ public AlignmentEvent(Object src, int location, AlignmentEventType type)
+ {
+ super(src); // set the source of the event by calling the parent
+ this.start = location;
+ this.end = location;
+ this.type = type;
+ }
+
+ /**
+ * Constructor to set the event source, location and type. The location
+ * is split into a start and end location.
+ *
+ * @param src the source of the event (i.e: the MSA)
+ * @param start the start location of the event
+ * @param end the end location of the event
+ * @param type the multiple sequence event type
+ */
+ public AlignmentEvent(Object src, int start, int end, AlignmentEventType type)
+ {
+ super(src); // set the source of the event by calling the parent
+ this.start = start;
+ this.end = end;
+ this.type = type;
+ }
+
+ /**
+ * Returns the start location of the event.
+ *
+ * @return the start
+ */
+ public int getStart()
+ {
+ return this.start;
+ }
+
+ /**
+ * Returns the end location of the event.
+ *
+ * @return the end
+ */
+ public int getEnd()
+ {
+ return this.end;
+ }
+
+ /**
+ * Returns the multiple sequence event type.
+ *
+ * @return the event type
+ */
+ public AlignmentEventType getType()
+ {
+ return this.type;
+ }
+} // AlignmentEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentEvent.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/10/31 15:50:28 lord
+ * Improved documentation
+ *
+ * Revision 1.1 2000/03/02 19:22:13 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.java b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.java
new file mode 100644
index 0000000..6e84181
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventProvider.java
@@ -0,0 +1,88 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+
+
+/**
+ * AlignmentEventProvider.java
+ *
+ *
+ * Created: Mon Apr 24 16:59:55 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentEventProvider.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface AlignmentEventProvider
+{
+ /**
+ * Add a listener specifically interested in events connected with the MSA.
+ *
+ * @param listener a multiple sequence alignment listener
+ */
+ public void addAlignmentListener( AlignmentListener listener );
+
+ /**
+ * Removes a multiple sequence alignment listener.
+ *
+ * @param listener the listener to be removed
+ */
+ public void removeAlignmentListener( AlignmentListener listener );
+
+ /**
+ * Adds a listener interested in vetoing multiple sequence alignment
+ * specific events.
+ *
+ * @param listener a vetoable multiple sequence alignment listener
+ */
+ public void addVetoableAlignmentListener
+ ( VetoableAlignmentListener listener );
+
+ /**
+ * Removes a vetoable multiple sequence alignment listener.
+ *
+ * @param listener the listener to be removed
+ */
+ public void removeVetoableAlignmentListener
+ ( VetoableAlignmentListener listener );
+} // AlignmentEventProvider
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentEventProvider.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/05/08 16:23:25 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.java b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.java
new file mode 100644
index 0000000..3a415e9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentEventType.java
@@ -0,0 +1,116 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+
+/**
+ * AlignmentEventType.java
+ *
+ * This class provides an enumerated type for the AlignmentEvent class
+ * to pass around as an identifier
+ *
+ * Created: Tue Feb 15 20:26:54 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentEventType.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public final class AlignmentEventType
+{
+ //Enum support
+ private String toString;
+ private AlignmentEventType( String toString )
+ {
+ this.toString = toString;
+ }
+
+ public String toString()
+ {
+ return super.toString() + " : Type " + toString;
+ }
+
+ //EventTypes
+
+ /**
+ * Event type indicating a new sequence has been added to the
+ * sequence alignment
+ */
+ public static final AlignmentEventType INSERT = new AlignmentEventType( "Insertion" );
+
+ /**
+ * Event type indicated a sequence has been removed from the
+ * sequence alignment
+ */
+ public static final AlignmentEventType DELETE = new AlignmentEventType( "Deletion" );
+
+ /**
+ * Event type indicating a change in the inset/preceeding number of gaps
+ */
+ public static final AlignmentEventType INSET_CHANGE = new AlignmentEventType( "Inset changed" );
+
+ /**
+ * Event type indicating that the length of the alignment has
+ * changed.
+ */
+ public static final AlignmentEventType LENGTH_CHANGE = new AlignmentEventType( "Length changed" );
+
+ /**
+ * This type says that the alignment has changed in some unknown
+ * way. This is very useful when its hard to work out what has
+ * changed. Its probably going to be fairly inefficient as well, and
+ * should be removed when feasible so that optimisations are possible.
+ */
+ public static final AlignmentEventType UNSPECIFIED = new AlignmentEventType( "Unspecified change" );
+
+}// AlignmentEventType
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentEventType.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/03/12 16:49:45 lord
+ * Added documentation and new type
+ *
+ * Revision 1.4 2000/06/13 11:06:35 lord
+ * Added new event type
+ *
+ * Revision 1.3 2000/03/27 18:48:34 lord
+ * Added Length change event
+ *
+ * Revision 1.2 2000/03/17 18:25:21 jns
+ * adding a new event to indicate the change of the inset.
+ *
+ * Revision 1.1 2000/03/02 19:22:30 jns
+ * initial code.
+ *
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.java b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.java
new file mode 100644
index 0000000..00979c7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListener.java
@@ -0,0 +1,69 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+import java.util.EventListener;
+
+
+/**
+ * AlignmentListener.java
+ *
+ * Objects of this type should be signalled after a change has occured
+ * to a multiple sequence alignment
+ * @see VetoableAlignmentListener
+ *
+ * Created: Tue Feb 15 19:51:22 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AlignmentListener.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface AlignmentListener extends EventListener
+{
+ /**
+ * method signalled after a change has occured to a multiple alignment
+ * @param event the event type
+ */
+ public void changeOccurred( AlignmentEvent event );
+
+}// AlignmentListener
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentListener.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/02 19:22:48 jns
+ * initial code.
+ *
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.java b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.java
new file mode 100644
index 0000000..6d63de3
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentListenerSupport.java
@@ -0,0 +1,158 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+import java.util.Vector;
+import java.util.Enumeration;
+
+
+/**
+ * AlignmentListenerSupport.java
+ *
+ * This class provides support and handles the listeners to a multiple
+ * seqyence alignment.
+ * @see AbstractMultipleSequenceAlignment
+ *
+ * Created: Thu Feb 17 14:57:37 2000
+ *
+ * @author J Selley
+ * @version $Id: AlignmentListenerSupport.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentListenerSupport
+{
+ private Vector listeners, vetoableListeners;
+
+ public AlignmentListenerSupport()
+ {
+ listeners = new Vector();
+ vetoableListeners = new Vector();
+ }
+
+ /**
+ * This function fires the MSA event to all the interested listeners, and also
+ * signals the vetoable listeners, which are stored separately. This is
+ * because the VetoableMultipleSequenceListener interface extends the
+ * MultipleSequenceListener interface.
+ * @see VetoableAlignmentListener
+ * @see AlignmentListener
+ *
+ * @param event the multiple sequence event
+ */
+ public void fireAlignmentEvent(AlignmentEvent event)
+ {
+ // enumerate through the listeners and exec the changeOccured function
+ for (Enumeration i = listeners.elements(); i.hasMoreElements(); ) {
+ ((AlignmentListener)i.nextElement()).changeOccurred(event);
+ }
+ // also enumerate through the vetoable listeners
+ // NB: VetoableMultipleSequenceListener extends MultipleSequenceListener
+ for (Enumeration i = vetoableListeners.elements(); i.hasMoreElements(); ) {
+ ((VetoableAlignmentListener)i.nextElement()).changeOccurred(event);
+ }
+ }
+
+ /**
+ * Notifies the vetoable listeners of a MSA vetoable event.
+ *
+ * @param event the vetoable multiple sequence event
+ */
+ public void fireVetoableAlignmentEvent(VetoableAlignmentEvent event)
+ throws AlignmentVetoException
+ {
+ // enumerates through the listeners, notifying them of the change
+ for (Enumeration i = vetoableListeners.elements(); i.hasMoreElements(); ) {
+ ((VetoableAlignmentListener)i.nextElement()).vetoableChangeOccurred(event);
+ }
+ }
+
+ /**
+ * Adds a alignment listener to a Vector of listeners.
+ *
+ * @param listener the listener to be added
+ */
+ public void addAlignmentListener(AlignmentListener listener)
+ {
+ if (listeners.contains(listener)) return;
+ else listeners.addElement(listener);
+ }
+
+ /**
+ * Removes a listener from the Vector.
+ *
+ * @param listener the listener to be removed
+ */
+ public void removeAlignmentListener(AlignmentListener listener)
+ {
+ listeners.removeElement(listener);
+ }
+
+ /**
+ * Adds a vetoable alignment listener to the Vector of vetoable
+ * listeners.
+ *
+ * @param listener the vetoable listener to be added.
+ */
+ public void addVetoableAlignmentListener
+ (VetoableAlignmentListener listener)
+ {
+ if (vetoableListeners.contains(listener)) return;
+ else vetoableListeners.addElement(listener);
+ }
+
+ /**
+ * Removes a vetoable alignment listener.
+ *
+ * @param listener the listener to be removed
+ */
+ public void removeVetoableAlignmentListener
+ (VetoableAlignmentListener listener)
+ {
+ vetoableListeners.removeElement(listener);
+ }
+} // AlignmentListenerSupport
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentListenerSupport.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/06/13 11:06:20 lord
+ * Fixed bug in vetoable fire method
+ *
+ * Revision 1.2 2000/03/10 17:53:35 lord
+ * Small bug fixes in firing methods
+ *
+ * Revision 1.1 2000/03/02 19:23:04 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.java b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.java
new file mode 100644
index 0000000..4389f2e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/AlignmentVetoException.java
@@ -0,0 +1,83 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+
+
+/**
+ * AlignmentVetoExcception.java
+ *
+ * An exception thrown when an object vetos an alignment event.
+ *
+ * Created: Tue Feb 15 21:16:35 2000
+ *
+ * @author J Selley
+ * @version $Id: AlignmentVetoException.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AlignmentVetoException extends Exception
+{
+ private AlignmentEvent event;
+
+ /**
+ * Constructor; includes reference to the event which spawned the veto.
+ */
+ public AlignmentVetoException(String message, AlignmentEvent event)
+ {
+ super( message );
+ this.event = event;
+ }
+
+ /**
+ * Returns the multiple sequence event that spawned the veto.
+ *
+ * @return the event
+ */
+ public AlignmentEvent getEvent()
+ {
+ return event;
+ }
+} // AlignmentVetoExcception
+
+
+
+/*
+ * ChangeLog
+ * $Log: AlignmentVetoException.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/09 16:42:13 lord
+ * Package update
+ *
+ * Revision 1.1 2000/03/02 19:23:21 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.java b/src/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.java
new file mode 100644
index 0000000..c4d9c3b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentEvent.java
@@ -0,0 +1,72 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+
+/**
+ * VetoableAlignmentEvent.java
+ *
+ * An event that may be vetoed by a listener.
+ *
+ * Created: Fri Feb 18 17:41:04 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: VetoableAlignmentEvent.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class VetoableAlignmentEvent extends AlignmentEvent
+{
+
+ public VetoableAlignmentEvent(Object src, int location,
+ AlignmentEventType type)
+ {
+ super( src, location, type );
+ }
+
+ public VetoableAlignmentEvent(Object src, int start, int end,
+ AlignmentEventType type)
+ {
+ super( src, start, end, type );
+ }
+
+} // VetoableAlignmentEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: VetoableAlignmentEvent.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/02 19:23:34 jns
+ * initial code.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.java b/src/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.java
new file mode 100644
index 0000000..603f093
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/alignment/event/VetoableAlignmentListener.java
@@ -0,0 +1,76 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.alignment.event; // Package name inserted by JPack
+
+
+/**
+ * VetoableAlignmentListener.java
+ *
+ * Listeners of this type are informed before a change takes place,
+ * and throw an exception if they so wish. Following this a second
+ * event is signalled to listeners of type AlignmentListener after
+ * the change has occured. Because two events are signalled it
+ * is not necessary to signal all VetoableAlignmentListener that a
+ * change has not occured.
+ *
+ * Created: Tue Feb 15 20:06:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: VetoableAlignmentListener.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface VetoableAlignmentListener extends AlignmentListener
+{
+ /**
+ * Method called before a change occurs to an alignment
+ *
+ * @param event
+ * @exception AlignmentVetoException
+ */
+ public void vetoableChangeOccurred( VetoableAlignmentEvent event )
+ throws AlignmentVetoException;
+
+}// VetoableMultipleSequenceListener
+
+
+/*
+ * ChangeLog
+ * $Log: VetoableAlignmentListener.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/03/10 13:40:06 jns
+ * changing event type from AlignmentEvent to a vetoable one.
+ *
+ * Revision 1.1 2000/03/02 19:23:48 jns
+ * initial code.
+ *
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.java b/src/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.java
new file mode 100644
index 0000000..a858e80
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequence.java
@@ -0,0 +1,178 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.AbstractMutableSequence;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.InvalidSequenceTypeException;
+import uk.ac.man.bioinf.sequence.complex.ComplexSequenceType;
+import uk.ac.man.bioinf.sequence.event.SequenceEventType;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+
+
+/**
+ * AbstractComplexSequence.java
+ *
+ *
+ * Created: Fri Nov 24 13:33:32 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractComplexSequence extends AbstractMutableSequence implements ComplexSequence
+{
+ private ComplexSequenceType type;
+
+ public AbstractComplexSequence( ComplexSequenceType type )
+ {
+ super( type );
+ this.type = type;
+ }
+
+ public ComplexSequenceType getComplexType()
+ {
+ return type;
+ }
+
+ protected void checkSequenceType( Element[] element ) throws InvalidSequenceTypeException
+ {
+ for( int i = 0; i < element.length; i++ ){
+ checkSequenceType( element[ i ] );
+ }
+ }
+
+ protected void checkSequenceType( Element element ) throws InvalidSequenceTypeException
+ {
+ if( !(element instanceof ComplexElement) ){
+ super.checkSequenceType( element );
+ }
+ else{
+ checkComplexSequenceType( (ComplexElement)element );
+ }
+ }
+
+ protected void checkComplexSequenceType( ComplexElement[] element ) throws InvalidSequenceTypeException
+ {
+ for( int i = 0; i < element.length; i++ ){
+ checkComplexSequenceType( element[ i ] );
+ }
+ }
+
+ protected void checkComplexSequenceType( ComplexElement element ) throws InvalidSequenceTypeException
+ {
+ if( !type.isAllowableElement( element ) ){
+ throw getComplexSequenceTypeException( element );
+ }
+ }
+
+ protected InvalidSequenceTypeException getComplexSequenceTypeException( Element element )
+ {
+ return new InvalidSequenceTypeException
+ ( "Element " + element + " is not a valid part of the complex sequence type " +
+ type.toString() );
+ }
+
+ public ComplexElement addModificationAt( Modification mod, int index ) throws SequenceVetoException
+ {
+ ComplexElement elem = getComplexElementAt( index );
+ ComplexElement newElem = ComplexElementFactory.addComplexElement
+ ( elem, mod );
+
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, SequenceEventType.SET );
+
+ fireVetoableSequenceEvent( event );
+ setElementAtQuietly( newElem, index );
+ fireSequenceEvent( event );
+
+ return newElem;
+ }
+
+ protected abstract ComplexElement setElementAtQuietly( ComplexElement element, int index );
+
+ public ComplexElement removeModificationAt( Modification mod, int index ) throws SequenceVetoException
+ {
+ ComplexElement elem = getComplexElementAt( index );
+ ComplexElement newElem = ComplexElementFactory.removeComplexElement
+ ( elem, mod );
+
+ VetoableSequenceEvent event = new VetoableSequenceEvent
+ ( this, index, SequenceEventType.SET );
+
+ fireVetoableSequenceEvent( event );
+ setElementAtQuietly( newElem, index );
+ fireSequenceEvent( event );
+
+ return newElem;
+ }
+
+ public char[] getComplexElementAtAsChar( int index )
+ {
+ ComplexElement elem = getComplexElementAt( index );
+ Modification[] mods = elem.getModifications();
+
+ char[] chars = new char[ mods.length + 2 ];
+
+ chars[ 0 ] = elem.toChar();
+
+ for( int i = 0; i < mods.length; i++ ){
+ chars[ i + 1 ] = mods[ i ].toChar();
+ }
+ chars[ chars.length - 1 ] = '_';
+
+ return chars;
+ }
+
+ public char[] getComplexSequenceAsChars()
+ {
+ // we don't know how long this is going to be before we do it.
+ StringBuffer buf = new StringBuffer();
+ for( int i = 0; i < getLength(); i++ ){
+ buf.append( getComplexElementAtAsChar( i + 1 ) );
+ }
+
+ return buf.toString().toCharArray();
+ }
+} // AbstractComplexSequence
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractComplexSequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.java b/src/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.java
new file mode 100644
index 0000000..706cb8c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/AbstractComplexSequenceType.java
@@ -0,0 +1,114 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Residue;
+import java.util.Arrays;
+import uk.ac.man.bioinf.sequence.types.AbstractSequenceType;
+
+/**
+ * AbstractComplexSequenceType.java
+ *
+ *
+ * Created: Tue Feb 29 22:10:30 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractComplexSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractComplexSequenceType extends AbstractSequenceType
+ implements ComplexSequenceType
+{
+ private Modification[] modifications;
+
+ public AbstractComplexSequenceType( Residue[] residues, Modification modification, String name )
+ {
+ super( residues, name );
+ modifications = new Modification[ 1 ];
+ modifications[ 0 ] = modification;
+ }
+
+ public AbstractComplexSequenceType( Residue[] residues, Modification[] modifications, String name )
+ {
+ super( residues, name );
+ this.modifications = modifications;
+ // sort these to speed things up for boolean is methods
+ Arrays.sort( modifications );
+ }
+
+ public Modification[] getModifications()
+ {
+ Modification[] retn = new Modification[ modifications.length ];
+ System.arraycopy( modifications, 0, retn, 0, modifications.length );
+ return retn;
+ }
+
+ public boolean isModification( Modification mod )
+ {
+ return (Arrays.binarySearch( modifications, mod ) > 0);
+ }
+
+ public boolean isModification( Modification[] mod )
+ {
+ for( int i = 0 ; i < mod.length ; i++ ){
+ // iterate through and balk as soon as false
+ if( isModification( mod[ i ] ) ){
+ return false;
+ }
+ } //end for( i < modifications.length )
+ return true;
+ }
+
+ public boolean isAllowableElement( ComplexElement elem )
+ {
+ // if this Residue isnt allowable then neither is the elem.
+ if( !( isElement( elem.getResidue() ) ) ){
+ return false;
+ }
+
+ // if the elem is allowable are all of its modifications?
+ return isModification( elem.getModifications() );
+ }
+} // AbstractComplexSequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractComplexSequenceType.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/04/18 17:51:48 jns
+ * o changes madde because of files moved to types package.
+ *
+ * Revision 1.1 2000/03/01 14:33:07 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/AbstractModification.java b/src/uk/ac/man/bioinf/sequence/complex/AbstractModification.java
new file mode 100644
index 0000000..660e314
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/AbstractModification.java
@@ -0,0 +1,79 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * AbstractModification.java
+ *
+ *
+ * Created: Mon Feb 28 23:13:18 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractModification.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+class AbstractModification implements Modification
+{
+ private String name;
+ private char toChar;
+
+ public AbstractModification( String name, char toChar )
+ {
+ this.name = name;
+ this.toChar = toChar;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public char toChar()
+ {
+ return toChar;
+ }
+} // AbstractModification
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractModification.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/02/29 11:24:57 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ComplexElement.java b/src/uk/ac/man/bioinf/sequence/complex/ComplexElement.java
new file mode 100644
index 0000000..60f842c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ComplexElement.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Residue;
+import uk.ac.man.bioinf.sequence.Element;
+
+/**
+ * ComplexElement.java
+ *
+ *
+ * Created: Mon Feb 28 20:41:07 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexElement.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ComplexElement extends Element
+{
+ public Residue getResidue();
+
+ public boolean isModified( Modification mod );
+
+ public Modification[] getModifications();
+}// ComplexElement
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexElement.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/02/29 11:24:57 lord
+ * Initial Checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.java b/src/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.java
new file mode 100644
index 0000000..7386dc5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ComplexElementFactory.java
@@ -0,0 +1,125 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Residue;
+
+
+/**
+ * ComplexElementFactory.java
+ *
+ *
+ * Created: Tue Feb 29 00:21:47 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexElementFactory.java,v 1.6 2001/08/16 14:30:21 white Exp $
+ */
+
+public class ComplexElementFactory
+{
+ private static ComplexElementFactoryInterface fact = new WeakComplexElementFactory();
+
+ public static void setComplexElementFactory( ComplexElementFactoryInterface factory )
+ {
+ fact = factory;
+ }
+
+ public static ComplexElement getComplexElement( Residue elem )
+ {
+ return fact.getComplexElement( elem );
+ }
+
+ public static ComplexElement addComplexElement( Residue res, Modification mod )
+ {
+ return fact.addComplexElement( res, mod );
+ }
+
+ public static ComplexElement addComplexElement( ComplexElement elem, Modification mod )
+ {
+ return fact.addComplexElement( elem, mod );
+ }
+
+ public static ComplexElement[] addComplexElement( Residue[] res, Modification[] mod )
+ {
+ ComplexElement[] elements = new ComplexElement[res.length];
+ for (int i=0; i<res.length;i++) {
+ elements[i] = fact.addComplexElement( res[i], mod[i] );
+ }
+ return elements;
+ }
+
+ public static ComplexElement[] addComplexElement( ComplexElement[] res, Modification[] mod )
+ {
+ ComplexElement[] elements = new ComplexElement[res.length];
+ for (int i=0; i<res.length;i++) {
+ elements[i] = fact.addComplexElement( res[i], mod[i] );
+ }
+ return elements;
+ }
+
+ public static ComplexElement removeComplexElement( ComplexElement elem, Modification mod )
+ {
+ return fact.removeComplexElement( elem, mod );
+ }
+
+} // ComplexElementFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexElementFactory.java,v $
+ * Revision 1.6 2001/08/16 14:30:21 white
+ * Added new convenience methods
+ *
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.3 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.2 2000/03/01 14:24:46 lord
+ * Now an abstract factory
+ *
+ * Revision 1.1 2000/02/29 11:24:57 lord
+ * Initial Checkin
+ *
+ */
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.java b/src/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.java
new file mode 100644
index 0000000..779bf48
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ComplexElementFactoryInterface.java
@@ -0,0 +1,68 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Residue;
+
+/**
+ * ComplexElementFactoryInterface.java
+ *
+ *
+ * Created: Wed Mar 1 12:40:54 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexElementFactoryInterface.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ComplexElementFactoryInterface
+{
+ public ComplexElement getComplexElement( Residue res );
+
+ public ComplexElement addComplexElement( Residue res, Modification mod );
+
+ public ComplexElement addComplexElement( ComplexElement elem, Modification mod );
+
+ public ComplexElement removeComplexElement( ComplexElement elem, Modification mod );
+}// ComplexElementFactoryInterface
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexElementFactoryInterface.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/03/01 14:33:08 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ComplexSequence.java b/src/uk/ac/man/bioinf/sequence/complex/ComplexSequence.java
new file mode 100644
index 0000000..20f43ec
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ComplexSequence.java
@@ -0,0 +1,87 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.NoSuchSequenceElementException;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+
+/**
+ * ComplexSequence.java
+ *
+ *
+ * Created: Wed Nov 22 17:56:08 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ComplexSequence extends Sequence
+{
+ public ComplexElement addModificationAt( Modification mod, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException;
+
+ public ComplexElement removeModificationAt( Modification mod, int index )
+ throws NoSuchSequenceElementException, SequenceVetoException, NoSuchModificationException;
+
+ public ComplexElement getComplexElementAt( int index );
+
+ /**
+ * Representing a ComplexElement as a char is not a simple task. An
+ * Element can have any number of Modifications each of which comes
+ * with its own char representation. The following approach is
+ * used. Each Element is represented first by its own char
+ * representation, and then by its all of its modifications, and
+ * then finally by an underscore _, which acts as a standard
+ * terminator. Counting the number of underscores should show how
+ * many Elements there are.
+ * This is not meant to be a particular wonderfully parse-able
+ * format.
+ *
+ * @param index
+ * @return a <code>char[]</code> value
+ */
+ public char[] getComplexElementAtAsChar( int index );
+
+ public char[] getComplexSequenceAsChars();
+
+}// ComplexSequence
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexSequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.java b/src/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.java
new file mode 100644
index 0000000..5dc28f7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ComplexSequenceType.java
@@ -0,0 +1,97 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.SequenceType;
+
+
+/**
+ * ComplexSequenceType.java
+ *
+ *
+ * Created: Tue Feb 29 11:25:27 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ComplexSequenceType extends SequenceType
+{
+ /**
+ * Gets all of the Modifications which are allowable in this
+ * sequence type. This should be immutable for a given instance of this.
+ * @return the modifications
+ */
+ public Modification[] getModifications();
+
+ /**
+ * Is this modification one which is allowable in this sequence
+ * type. This should be immutable for a given instance of this.
+ * @param mod the modification
+ * @return true if the modification is allowable
+ */
+ public boolean isModification( Modification mod );
+
+ /**
+ * Are these modifications allowable in this sequence type. This
+ * should be immutable.
+ * @param mod the modifications
+ * @return true if all the modifications are allowable
+ */
+ public boolean isModification( Modification[] mod );
+
+ /**
+ * Is this given element allowable in this sequence type. A trivial
+ * implementation of this would simply check if the ComplexElement
+ * Residue is allowable, and all of the Modifications for this
+ * ComplexElement are allowable. However there are other
+ * possibilties if for instance not all Residues in a given sequence
+ * type are Modifiable by all the allowable modifications
+ * @param elem
+ * @return
+ */
+ public boolean isAllowableElement( ComplexElement elem );
+
+} // ComplexSequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexSequenceType.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/03/01 20:17:55 lord
+ * Lots of changes
+ *
+ * Revision 1.1 2000/03/01 14:33:08 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.java b/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.java
new file mode 100644
index 0000000..517c7c6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexElement.java
@@ -0,0 +1,168 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Residue;
+
+
+/**
+ * DefaultComplexElement.java
+ *
+ *
+ * Created: Mon Feb 28 20:42:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultComplexElement.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultComplexElement implements ComplexElement
+{
+ private Residue residue;
+ private ModificationSet modifications;
+
+ DefaultComplexElement()
+ {
+ }
+
+ // element implementation
+ public char toChar()
+ {
+ return residue.toChar();
+ }
+
+ // These methods are all package access because a ComplexElement
+ // should really be immutable once it has been created. The problem
+ // is with this is that it means we have to create a new
+ // ComplexElement for each look up which is a waste of time. This
+ // way we only create a new ComplexElement when we need a new one...
+ void setResidue( Residue residue )
+ {
+ this.residue = residue;
+ }
+
+ void setModifications( Modification[] mods, Modification mod )
+ {
+ modifications = ModificationSetFactory.getModificationSet( mods, mod );
+ }
+
+ void setModifications( Modification[] mod )
+ {
+ modifications = ModificationSetFactory.getModificationSet( mod );
+ }
+
+ void setModifications( Modification mod )
+ {
+ modifications = ModificationSetFactory.getModificationSet( mod );
+ }
+
+ void setModifications()
+ {
+ modifications = ModificationSetFactory.getModificationSet();
+ }
+
+ // I originally put this method in, and leave it here to remind
+ // myself not to do it. It would almost certainly be a mistake as
+ // alterations to this, would also percolate through to the object
+ // passed as a parameter. Which is almost certainly guarenteed to be
+ // a mistake.
+ /*
+ void setModifications( DefaultComplexElement elem )
+ {
+ this.modifications = elem.modifications;
+ }
+ */
+
+ public Residue getResidue()
+ {
+ return residue;
+ }
+
+ public Modification[] getModifications()
+ {
+ return modifications.getModifications();
+ }
+
+ public boolean isModified( Modification mod )
+ {
+ return modifications.containsModification( mod );
+ }
+
+ public boolean equals( Object obj )
+ {
+ // if these are not of the same type they are not the
+ // same. Obviously.
+ if( !( obj instanceof DefaultComplexElement ) ){
+ return false;
+ }
+
+ // cast it down. Reasons to hate java?
+ DefaultComplexElement elem = (DefaultComplexElement)obj;
+
+ // if they contain a different Residue then return false. Residues
+ // are considered equal if they are == therefore this is okay!
+ if( elem.residue != this.residue ) return false;
+
+ // if its got this far then are all the modifications equal
+ return elem.modifications.equals( this.modifications );
+ }
+
+ public int hashCode()
+ {
+ // we dont really care if this overflows, as a wrapped around
+ // hashcode is just as good a hash code.
+ return residue.hashCode() + modifications.hashCode();
+ }
+} // DefaultComplexElement
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultComplexElement.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.4 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.3 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.2 2000/03/01 14:25:50 lord
+ * Now uses factory based Modification Sets
+ *
+ * Revision 1.1 2000/02/29 11:24:57 lord
+ * Initial Checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.java b/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.java
new file mode 100644
index 0000000..f116882
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequence.java
@@ -0,0 +1,141 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import java.util.ArrayList;
+import java.util.Arrays;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Residue;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+
+
+/**
+ * DefaultComplexSequence.java
+ *
+ *
+ * Created: Fri Nov 24 14:08:23 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultComplexSequence.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultComplexSequence extends AbstractComplexSequence
+{
+ private ArrayList elements;
+ private Identifier ident;
+
+ public DefaultComplexSequence( Residue[] elements, ComplexSequenceType type, Identifier identifier )
+ {
+ super( type );
+
+ checkSequenceType( elements );
+
+ this.ident = ident;
+
+ ComplexElement[] complex = Sequences.getResiduesAsComplexElements( elements );
+ this.elements = new ArrayList( Arrays.asList( complex ) );
+ }
+
+ public DefaultComplexSequence( ComplexElement[] elements, ComplexSequenceType type, Identifier identifier )
+ {
+ super( type );
+
+ checkComplexSequenceType( elements );
+ this.ident = ident;
+
+ this.elements = new ArrayList( Arrays.asList( elements ) );
+ }
+
+ public Identifier getIdentifier()
+ {
+ return ident;
+ }
+
+ public Element getElementAt( int index )
+ {
+ return getComplexElementAt( index ).getResidue();
+ }
+
+ public ComplexElement getComplexElementAt( int index )
+ {
+ return (ComplexElement)elements.get( index - 1 );
+ }
+
+ public int getLength()
+ {
+ return elements.size();
+ }
+
+ public ComplexElement[] getSequenceAsComplexElements()
+ {
+ Object[] elemObjs = elements.toArray();
+ ComplexElement[] elems = new ComplexElement[ elemObjs.length ];
+
+ System.arraycopy( elemObjs, 0, elems, 0, elemObjs.length );
+ return elems;
+ }
+
+ public Element[] getSequenceAsElements()
+ {
+ // get the elements, and make the destination array
+ Object[] elemObjs = elements.toArray();
+ Element[] elems = new Element[ elemObjs.length ];
+
+ // do the copy to array of appropriate type and return it
+ System.arraycopy( elemObjs, 0, elems, 0, elemObjs.length );
+ return elems;
+ }
+
+ protected ComplexElement setElementAtQuietly( ComplexElement elem, int index )
+ {
+ checkComplexSequenceType( elem );
+ elements.set( index - 1, elem );
+ return elem;
+ }
+
+}// DefaultComplexSequence
+
+/*
+ * ChangeLog
+ * $Log: DefaultComplexSequence.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/13 16:35:25 lord
+ * Some implementation moved to Sequences static class
+ *
+ * Revision 1.1 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ */
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.java b/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.java
new file mode 100644
index 0000000..b9d3985
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/DefaultComplexSequenceType.java
@@ -0,0 +1,143 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.SequenceType;
+
+
+/**
+ * DefaultComplexSequenceType.java
+ *
+ *
+ * Created: Mon Nov 27 16:05:27 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultComplexSequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultComplexSequenceType implements ComplexSequenceType
+{
+ private Modification[] mods;
+ private SequenceType type;
+ private String name;
+
+ public DefaultComplexSequenceType( SequenceType type, Modification[] mods, String name )
+ {
+ this.type = type;
+ this.mods = mods;
+ this.name = name;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public Modification[] getModifications()
+ {
+ return ((Modification[])mods.clone());
+ }
+
+ public boolean isModification( Modification mod )
+ {
+ // if there were lots of Modifications we could probably speed
+ // this up with a hash look up.
+ for( int i = 0; i < mods.length; i++ ){
+ if( mods[ i ].equals( mod ) ){
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ public boolean isModification( Modification[] mods )
+ {
+ for( int i = 0; i < mods.length; i++ ){
+ if( !isModification( mods[ i ] ) ){
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public boolean isAllowableElement( ComplexElement element )
+ {
+ return
+ ( type.isElement( element.getResidue() ) &&
+ isModification( element.getModifications() ));
+ }
+
+ // Code for delegation of uk.ac.man.bioinf.sequence.SequenceType methods to type
+ public boolean isElement(Element[] param1) {
+ return type.isElement(param1);
+ }
+
+ public boolean isElement(char[] param1) {
+ return type.isElement(param1);
+ }
+
+ public boolean isElement(Element param1) {
+ return type.isElement(param1);
+ }
+
+ public boolean isElement(char param1) {
+ return type.isElement(param1);
+ }
+
+ public Element[] getElements() {
+ return type.getElements();
+ }
+
+ public Element getElementForInt(int param1) {
+ return type.getElementForInt(param1);
+ }
+
+ public int getIntForElement(Element param1) {
+ return type.getIntForElement(param1);
+ }
+
+ public int size() {
+ return type.size();
+ }
+} // DefaultComplexSequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultComplexSequenceType.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.java b/src/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.java
new file mode 100644
index 0000000..7a413d8
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/DefaultGappedComplexSequence.java
@@ -0,0 +1,267 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.AbstractMutableSequence;
+import uk.ac.man.bioinf.sequence.AbstractSequence;
+import uk.ac.man.bioinf.sequence.DefaultSequence;
+import uk.ac.man.bioinf.sequence.EditableSequence;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.InvalidSequenceTypeException;
+import uk.ac.man.bioinf.sequence.Residue;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.util.IntArrayList;
+
+
+/**
+ * DefaultGappedComplexSequence.java
+ *
+ *
+ * Created: Tue Dec 5 16:55:11 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultGappedComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultGappedComplexSequence extends AbstractComplexSequence
+ implements GappedComplexSequence
+{
+
+ // This carries contains the Gap model that we are using, and
+ // provides access to the GappedSequence model
+ private DisabledDefaultGappedSequence gappedSequence;
+
+ // this element array contains the complex elements. Its also the
+ // underlying data structure (as an Element array) for the ungapped
+ // sequences elements in the DefaultGappedComplexSequence.
+ private ComplexElement[] elements;
+
+ public DefaultGappedComplexSequence( Element[] elements, ComplexSequenceType type )
+ {
+ super( type );
+
+ IntArrayList list = DefaultGappedSequence.getGapModelForElements( elements );
+
+ Sequences.printElements( elements );
+ System.out.println( list.get( list.size() - 1 ) );
+
+ Residue[] strippedElements = DefaultGappedSequence.stripGapsFromElements
+ ( elements, list.get( 0 ) );
+
+ ComplexElement[] strippedComplexElements = Sequences.getResiduesAsComplexElements( strippedElements );
+
+ this.elements = strippedComplexElements;
+
+
+ DefaultSequence sequence = new DefaultSequence( strippedComplexElements, null ){
+ public void checkSequenceType( Element[] elems ) throws InvalidSequenceTypeException
+ {
+ // no implementation okay
+ }
+ };
+
+ gappedSequence = new DisabledDefaultGappedSequence
+ ( sequence, list );
+ }
+
+ public ComplexElement getComplexElementAt( int index )
+ {
+ return (ComplexElement)gappedSequence.getElementAt( index );
+ }
+
+ public Element getElementAt( int index )
+ {
+ return getComplexElementAt( index ).getResidue();
+ }
+
+ public Element getGappedElementAt( int index )
+ {
+ int ungappedIndex = gappedSequence.getUngappedPositionOf( index );
+
+ if( ungappedIndex < 1 ){
+ return Gap.GAP;
+ }
+
+ return getElementAt( ungappedIndex );
+ }
+
+ public ComplexElement[] getSequenceAsComplexElements()
+ {
+ // this is returning an array which actually contains
+ // ComplexElements
+ Element[] elems = gappedSequence.getSequenceAsElements();
+
+ ComplexElement[] complexElems = new ComplexElement[ elems.length ];
+
+ System.arraycopy( elems, 0, complexElems, 0, elems.length );
+ return complexElems;
+ }
+
+ protected ComplexElement setElementAtQuietly( ComplexElement elem, int index )
+ {
+ checkComplexSequenceType( elem );
+ elements[ index - 1 ] = elem;
+ return elem;
+ }
+
+ public Identifier getIdentifier() {
+ // (PENDING:- PL) write this.
+ return gappedSequence.getIdentifier();
+ }
+
+
+
+
+ /**
+ * This class provides us with the data model for holding all of the
+ * elements, and means that we can reuse the GapModel of the
+ * GappedSequence implementation. One problem is that the
+ * SequenceType of the super class gets in the way. We want to store
+ * ComplexElements which are not part of the sequence type. So we
+ * need to disable the type checking mechanism.
+ *
+ * We also need to ensure that the event mechanism is not to
+ * wasteful, and disable most of this as well
+ *
+ */
+ class DisabledDefaultGappedSequence extends DefaultGappedSequence
+ {
+ DisabledDefaultGappedSequence( Sequence seq, IntArrayList toGappedMap )
+ {
+ super( seq, toGappedMap );
+ }
+
+ protected void checkSequenceType( Element element ) throws InvalidSequenceTypeException
+ {
+ //empty definition okay!
+ }
+
+ protected void checkSequenceType( Element[] elements ) throws InvalidSequenceTypeException
+ {
+ //empty definition okay
+ }
+ }
+
+ // Code for delegation of uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence methods to gappedSequence
+ public GappedSequence getElementsAsGappedSequence(Element[] param1, SequenceType param2, Identifier param3) {
+ return gappedSequence.getElementsAsGappedSequence(param1, param2, param3);
+ }
+
+ public GappedSequence getElementsAsGappedSequence(Element[] param1, SequenceType param2) {
+ return gappedSequence.getElementsAsGappedSequence(param1, param2);
+ }
+
+ public Element[] getSequenceAsElements() {
+ return gappedSequence.getSequenceAsElements();
+ }
+
+ public int getLength() {
+ return gappedSequence.getLength();
+ }
+
+ public GappedSequence getGappedSubSequence(int param1, int param2) {
+ return gappedSequence.getGappedSubSequence(param1, param2);
+ }
+
+
+ public Element[] getGappedSequenceAsElements() {
+ return gappedSequence.getGappedSequenceAsElements();
+ }
+
+ public int getGappedLength() {
+ return gappedSequence.getGappedLength();
+ }
+
+ public int getGappedPositionOf(int param1) {
+ return gappedSequence.getGappedPositionOf(param1);
+ }
+
+ public int getUngappedPositionOf(int param1) {
+ return gappedSequence.getUngappedPositionOf(param1);
+ }
+ // Code for delegation of uk.ac.man.bioinf.sequence.alignment.AbstractGappedSequence methods to gappedSequence
+
+ public void insertGapAt(int param1) throws SequenceVetoException {
+ gappedSequence.insertGapAt(param1);
+ }
+
+ public void insertGapAt(int param1, int param2) throws SequenceVetoException {
+ gappedSequence.insertGapAt(param1, param2);
+ }
+
+ public void deleteGapAt(int param1) throws SequenceVetoException {
+ gappedSequence.deleteGapAt(param1);
+ }
+
+ public void deleteGapAt(int param1, int param2) throws SequenceVetoException {
+ gappedSequence.deleteGapAt(param1, param2);
+ }
+
+ public char getGappedElementAtAsChar(int param1) {
+ return gappedSequence.getGappedElementAtAsChar(param1);
+ }
+
+ public char[] getGappedSequenceAsChars() {
+ return gappedSequence.getGappedSequenceAsChars();
+ }
+
+ // Code for delegation of uk.ac.man.bioinf.sequence.AbstractSequence methods to gappedSequence
+ public Sequence getSubSequence(int param1, int param2) {
+ return gappedSequence.getSubSequence(param1, param2);
+ }
+
+ public char[] getSequenceAsChars() {
+ return gappedSequence.getSequenceAsChars();
+ }
+
+ public char getElementAtAsChar(int param1) {
+ return gappedSequence.getElementAtAsChar(param1);
+ }
+} // DefaultGappedComplexSequence
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultGappedComplexSequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/13 16:35:41 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.java b/src/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.java
new file mode 100644
index 0000000..c110606
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/GappedComplexSequence.java
@@ -0,0 +1,59 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+/**
+ * GappedComplexSequence.java
+ *
+ * Place holder type interface.
+ *
+ * Created: Tue Dec 5 16:55:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GappedComplexSequence.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface GappedComplexSequence extends GappedSequence, ComplexSequence
+{
+
+}// GappedComplexSequence
+
+
+/*
+ * ChangeLog
+ * $Log: GappedComplexSequence.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/13 16:35:41 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/GenericModification.java b/src/uk/ac/man/bioinf/sequence/complex/GenericModification.java
new file mode 100644
index 0000000..225456c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/GenericModification.java
@@ -0,0 +1,82 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * GenericModification.java
+ *
+ *
+ * Created: Mon Feb 28 20:58:20 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GenericModification.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+class GenericModification extends AbstractModification
+{
+ GenericModification( String name, char toChar )
+ {
+ super( name, toChar );
+ }
+
+ // these two methods just defer to the string
+ public boolean equals( Object obj )
+ {
+ if( !( obj instanceof GenericModification ) ) return false;
+
+ return getName().equals( ((GenericModification)obj).getName() );
+ }
+
+ public int hashCode()
+ {
+ return getName().hashCode();
+ }
+} // GenericModification
+
+
+
+/*
+ * ChangeLog
+ * $Log: GenericModification.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.2 2000/03/01 14:26:41 lord
+ * Fixed bug in equals
+ *
+ * Revision 1.1 2000/02/29 11:24:58 lord
+ * Initial Checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/HardComplexElementFactory.java b/src/uk/ac/man/bioinf/sequence/complex/HardComplexElementFactory.java
new file mode 100644
index 0000000..6c7996a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/HardComplexElementFactory.java
@@ -0,0 +1,144 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Residue;
+import java.util.Map;
+import java.util.HashMap;
+
+
+/**
+ * HardComplexElementFactory.java
+ *
+ *
+ * Created: Tue Feb 29 00:21:47 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: HardComplexElementFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+class HardComplexElementFactory
+{
+ // its in here that we keep a modification which is used each time
+ // we do a get call. This way we dont have to instantiate a new
+ // object for every get, only those where a previously cached object
+ // is not found
+ private DefaultComplexElement cachedElement;
+ private Map complexElements = new HashMap();
+
+ public ComplexElement getComplexElement( Residue res, Modification mod )
+ {
+ // first we need a DefaultElement to be dealing withh
+ if( cachedElement == null ){
+ cachedElement = new DefaultComplexElement();
+ }
+
+ // now set this modification so that it looks like the one that we
+ // want.
+ cachedElement.setResidue( res );
+ cachedElement.setModifications( mod );
+
+ return getCachedComplexElement();
+ }
+
+ public ComplexElement getComplexElement( ComplexElement elem, Modification mod )
+ {
+ // do we need a new element
+ if( cachedElement == null ){
+ cachedElement = new DefaultComplexElement();
+ }
+
+ // we now want to set the Modification up to duplicate the old one
+ // (PENDING) I think that there is a problem here. Really this
+ // method should work whether for all objects of type
+ // ComplexElement. The problem is at the moment I havent
+ // adequately defined the notion of equality of two
+ // ComplexElements. Its not clear for instance whether two
+ // ComplexElements of different classes, but which contain
+ // indentical Residues and Modifications, should be equal.
+
+ cachedElement.setResidue( elem.getResidue() );
+ cachedElement.setModifications( elem.getModifications(), mod );
+
+ // now return the cached copy if it exists, or the one we have
+ // just created.
+ return getCachedComplexElement();
+ }
+
+ private ComplexElement getCachedComplexElement()
+ {
+ // See whether we already have this complex element???
+ ComplexElement retn = (ComplexElement)complexElements.get( cachedElement );
+
+ // We do already have this element, therefore return the one we
+ // already have, keeping the old one for later
+ if( retn != null ){
+ return retn;
+ }
+
+ // we dont already have this element, so store the one we have
+ // created and return that, make sure that we null the internal we
+ // are storing in this class so that we dont use it next time. We
+ // store it as the valued keyed on itself, so that we can retrieve
+ // this ComplexElement. The point of all this is that
+ // ComplexElements which are .equals() to each other should also
+ // therefore be == to each other outside of this package.
+ complexElements.put( cachedElement, cachedElement );
+ retn = cachedElement;
+ cachedElement = null;
+ return retn;
+ }
+} // HardComplexElementFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: HardComplexElementFactory.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.1 2000/03/01 14:33:08 lord
+ * Initial checkin
+ *
+ * Revision 1.1 2000/02/29 11:24:57 lord
+ * Initial Checkin
+ *
+ */
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.java b/src/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.java
new file mode 100644
index 0000000..3e4198f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/HardModificationSetFactory.java
@@ -0,0 +1,131 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.complex.ModificationSetFactoryInterface;
+import uk.ac.man.bioinf.sequence.complex.Modification;
+import java.util.Map;
+import java.util.HashMap;
+
+
+/**
+ * HardModificationSetFactory.java
+ *
+ *
+ * Created: Wed Mar 1 15:04:37 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: HardModificationSetFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class HardModificationSetFactory implements ModificationSetFactoryInterface
+{
+
+ private ModificationSet cachedSet;
+ private Map modificationSet = new HashMap();
+
+ public ModificationSet getModificationSet()
+ {
+ if( cachedSet == null ){
+ cachedSet = new ModificationSet();
+ }
+
+ cachedSet.setModification();
+ return getCachedModificationSet();
+ }
+
+ public ModificationSet getModificationSet(Modification modification )
+ {
+ if( cachedSet == null ){
+ cachedSet = new ModificationSet();
+ }
+
+ cachedSet.setModification( modification );
+ return getCachedModificationSet();
+ }
+
+ public ModificationSet getModificationSet(Modification[] modifications )
+ {
+ if( cachedSet == null ){
+ cachedSet = new ModificationSet();
+ }
+
+ cachedSet.setModification( modifications );
+ return getCachedModificationSet();
+ }
+
+ public ModificationSet getModificationSet(Modification[] modifications, Modification modification )
+ {
+ // make an array which is big enough.
+ int size = modifications.length;
+ Modification[] longModifications = new Modification[ size + 1 ];
+ // copy the old array across
+ System.arraycopy( modifications, 0, longModifications, 0, size );
+ // and stuff the new one in at then end
+ longModifications[ size ] = modification;
+
+ return getModificationSet( longModifications );
+ }
+
+ private ModificationSet getCachedModificationSet()
+ {
+ // do we already have a ModificationSet with this stuff in it?
+ ModificationSet retn = (ModificationSet)modificationSet.get( cachedSet );
+
+ // we do already have this element there return this one, and
+ // keep the cached on to use in the next query
+ if( retn != null ){
+ return retn;
+ }
+
+ // we dont already have this element so we store the one we have
+ // created, null the cachedReference so that we dont use it again,
+ // and then return it
+ modificationSet.put( cachedSet, cachedSet );
+ retn = cachedSet;
+ cachedSet = null;
+ return retn;
+ }
+} // HardModificationSetFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: HardModificationSetFactory.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/03/01 20:17:55 lord
+ * Lots of changes
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.java b/src/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.java
new file mode 100644
index 0000000..9656fc3
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/IllegalDuplicateModificationException.java
@@ -0,0 +1,62 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * IllegalDuplicateModificationException.java
+ *
+ *
+ * Created: Mon Feb 28 23:57:13 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: IllegalDuplicateModificationException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class IllegalDuplicateModificationException extends RuntimeException
+{
+
+ public IllegalDuplicateModificationException( String message )
+ {
+ super( message );
+ }
+} // IllegalDuplicateModificationException
+
+
+
+/*
+ * ChangeLog
+ * $Log: IllegalDuplicateModificationException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/02/29 11:24:58 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/Methylation.java b/src/uk/ac/man/bioinf/sequence/complex/Methylation.java
new file mode 100644
index 0000000..f028046
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/Methylation.java
@@ -0,0 +1,68 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * Methylation.java
+ *
+ *
+ * Created: Tue Feb 29 11:44:59 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Methylation.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class Methylation extends SingletonModification
+{
+
+ private Methylation( String name, char toChar )
+ {
+ super( name, toChar );
+ }
+
+ public static final Methylation METHYLATION = new Methylation( "Methylation", 'm' );
+} // Methylation
+
+
+
+/*
+ * ChangeLog
+ * $Log: Methylation.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/03/01 14:33:08 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/Modification.java b/src/uk/ac/man/bioinf/sequence/complex/Modification.java
new file mode 100644
index 0000000..e6af996
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/Modification.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+/**
+ * Modification.java
+ *
+ *
+ * Created: Mon Feb 28 20:42:16 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Modification.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Modification
+{
+ public String getName();
+
+ public char toChar();
+}// Modification
+
+
+/*
+ * ChangeLog
+ * $Log: Modification.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/02/29 11:24:58 lord
+ * Initial Checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ModificationFactory.java b/src/uk/ac/man/bioinf/sequence/complex/ModificationFactory.java
new file mode 100644
index 0000000..3fd4659
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ModificationFactory.java
@@ -0,0 +1,105 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import java.util.HashMap;
+
+
+/**
+ * ModificationFactory.java
+ *
+ *
+ * Created: Mon Feb 28 23:07:50 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ModificationFactory.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ModificationFactory
+{
+ private static HashMap modifications = new HashMap();
+
+ static void addNewSingletonModification( String name, SingletonModification modification )
+ {
+ if( modifications.containsKey( name ) )
+ throw new IllegalDuplicateModificationException
+ ( "Attempt to install singleton modification " + modification.getName() +
+ " conflicts with modification " + modifications.get( name ) );
+
+ modifications.put( name, modification );
+ }
+
+ static void addNewGenericModification( String name, GenericModification modification )
+ {
+ if( modifications.containsKey( name ) )
+ throw new IllegalDuplicateModificationException
+ ( "Attempt to generic singleton modification " + modification.getName() +
+ " conflicts with modification " + modifications.get( name ) );
+
+ modifications.put( name, modification );
+ }
+
+ public static Modification getModification( String name )
+ {
+ Object retn = modifications.get( name );
+ if( retn == null ) throw new NoSuchModificationException
+ ( "Attempt to recover modification of name " + name + " which does not exist. " +
+ "Use the ModificationFactory.createModification instead" );
+
+ return (Modification)retn;
+ }
+
+ public static Modification createModification( String name, char toChar )
+ {
+ // create a new modification
+ GenericModification mod = new GenericModification( name, toChar );
+ // and add it to the cache, also duplicate check
+ addNewGenericModification( name, mod );
+ return mod;
+ }
+} // ModificationFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModificationFactory.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.2 2000/03/01 14:27:36 lord
+ * cosmetic changes to string output
+ *
+ * Revision 1.1 2000/02/29 11:24:58 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ModificationSet.java b/src/uk/ac/man/bioinf/sequence/complex/ModificationSet.java
new file mode 100644
index 0000000..6ac1648
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ModificationSet.java
@@ -0,0 +1,143 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import java.util.Arrays;
+import java.util.Comparator;
+
+
+/**
+ * ModificationSet.java
+ *
+ *
+ * Created: Mon Feb 28 21:16:56 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ModificationSet.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+class ModificationSet
+{
+ // This array should always be sorted!!!
+ private Modification[] modifications;
+ private int hash = 0;
+ private boolean changed = true;
+
+ private static Comparator modificationComparator = new Comparator()
+ {
+ public int compare(Object param1, Object param2)
+ {
+ return ((Modification)param1).getName().compareTo( ((Modification)param2).getName() );
+ }
+ };
+
+ ModificationSet()
+ {
+ }
+
+ void setModification()
+ {
+ modifications = new Modification[ 0 ];
+ }
+
+ void setModification( Modification modification )
+ {
+ changed = true;
+ modifications = new Modification[ 1 ];
+ modifications[ 0 ] = modification;
+ }
+
+ void setModification( Modification[] modifications )
+ {
+ changed = true;
+ this.modifications = modifications;
+ // guarentee that array is sorted. This allows the equals
+ // comparison to be done at high speed.
+ Arrays.sort( this.modifications, modificationComparator );
+ }
+
+ boolean containsModification( Modification mod )
+ {
+ // this takes place in log n time. A hash table would be faster,
+ // but the getModifications, equals and hashCode methods will run
+ // in something greater than linear time (depending on the load of
+ // the hash). Also there is no waste of memory in storage here,
+ // where there is in a hash. And for small numbers of
+ // modifications the hash function will probably take longer than
+ // this search
+ return (Arrays.binarySearch( modifications, mod ) > 0);
+ }
+
+ Modification[] getModifications()
+ {
+ return modifications;
+ }
+
+ public boolean equals( Object obj )
+ {
+ if( !( obj instanceof ModificationSet ) ) return false;
+ return Arrays.equals( modifications, ((ModificationSet)obj).modifications);
+ }
+
+ public int hashCode()
+ {
+ if( changed ){
+ for( int i = 0; i < modifications.length; i++ ){
+ hash += modifications[ i ].hashCode();
+ }
+ changed = false;
+ }
+ return hash;
+ }
+} // ModificationSet
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModificationSet.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.4 2000/07/18 12:38:10 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.2 2000/03/01 14:30:46 lord
+ * Lots of changes so that this can be generated by a factory
+ *
+ * Revision 1.1 2000/02/29 11:24:58 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ModificationSetFactory.java b/src/uk/ac/man/bioinf/sequence/complex/ModificationSetFactory.java
new file mode 100644
index 0000000..db0a4d1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ModificationSetFactory.java
@@ -0,0 +1,89 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * ModificationSetFactory.java
+ *
+ *
+ * Created: Tue Feb 29 20:18:04 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ModificationSetFactory.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+class ModificationSetFactory
+{
+ private static ModificationSetFactoryInterface fact = new WeakModificationSetFactory();
+
+
+ static ModificationSet getModificationSet()
+ {
+ return fact.getModificationSet();
+ }
+
+ static ModificationSet getModificationSet( Modification modification )
+ {
+ return fact.getModificationSet( modification );
+ }
+
+ static ModificationSet getModificationSet( Modification[] modifications )
+ {
+ return fact.getModificationSet( modifications );
+ }
+
+ static ModificationSet getModificationSet( Modification[] modifications, Modification modification )
+ {
+ return fact.getModificationSet( modifications, modification );
+ }
+} // ModificationSetFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: ModificationSetFactory.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.3 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.2 2000/03/01 20:17:55 lord
+ * Lots of changes
+ *
+ * Revision 1.1 2000/03/01 14:33:08 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.java b/src/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.java
new file mode 100644
index 0000000..f816f9e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/ModificationSetFactoryInterface.java
@@ -0,0 +1,68 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+/**
+ * ModificationSetFactoryInterface.java
+ *
+ *
+ * Created: Wed Mar 1 15:01:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ModificationSetFactoryInterface.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ModificationSetFactoryInterface
+{
+ public ModificationSet getModificationSet();
+
+ public ModificationSet getModificationSet( Modification modification );
+
+ public ModificationSet getModificationSet( Modification[] modifications );
+
+ public ModificationSet getModificationSet( Modification[] modifications, Modification modification );
+
+}// ModificationSetFactoryInterface
+
+
+/*
+ * ChangeLog
+ * $Log: ModificationSetFactoryInterface.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/03/01 20:17:55 lord
+ * Lots of changes
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.java b/src/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.java
new file mode 100644
index 0000000..84489d6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/NoSuchModificationException.java
@@ -0,0 +1,61 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * NoSuchModificationException.java
+ *
+ *
+ * Created: Tue Feb 29 00:09:26 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NoSuchModificationException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NoSuchModificationException extends RuntimeException
+{
+ public NoSuchModificationException( String message )
+ {
+ super( message );
+ }
+} // NoSuchModificationException
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoSuchModificationException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/02/29 11:24:58 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/SingletonModification.java b/src/uk/ac/man/bioinf/sequence/complex/SingletonModification.java
new file mode 100644
index 0000000..3ff4395
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/SingletonModification.java
@@ -0,0 +1,69 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+
+
+/**
+ * SingletonModification.java
+ *
+ *
+ * Created: Mon Feb 28 23:16:04 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SingletonModification.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SingletonModification extends AbstractModification
+{
+ SingletonModification( String name, char toChar )
+ {
+ super( name, toChar );
+ ModificationFactory.addNewSingletonModification( name, this );
+ }
+} // SingletonModification
+
+
+
+/*
+ * ChangeLog
+ * $Log: SingletonModification.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.2 2000/03/01 14:32:02 lord
+ * cosmetic
+ *
+ * Revision 1.1 2000/02/29 11:24:45 lord
+ * Initial Checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/WeakComplexElementFactory.java b/src/uk/ac/man/bioinf/sequence/complex/WeakComplexElementFactory.java
new file mode 100644
index 0000000..f29a7ce
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/WeakComplexElementFactory.java
@@ -0,0 +1,188 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import java.lang.ref.WeakReference;
+import java.util.WeakHashMap;
+import uk.ac.man.bioinf.sequence.Residue;
+import uk.ac.man.bioinf.util.ArrayManipulation;
+
+
+/**
+ * WeakComplexElementFactory.java
+ *
+ *
+ * Created: Tue Feb 29 00:21:47 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: WeakComplexElementFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+class WeakComplexElementFactory implements ComplexElementFactoryInterface
+{
+ // its in here that we keep a modification which is used each time
+ // we do a get call. This way we dont have to instantiate a new
+ // object for every get, only those where a previously cached object
+ // is not found
+ private DefaultComplexElement cachedElement;
+
+ private WeakHashMap complexElements = new WeakHashMap();
+
+
+ public ComplexElement getComplexElement( Residue res )
+ {
+ if( cachedElement == null ){
+ cachedElement = new DefaultComplexElement();
+ }
+
+ cachedElement.setResidue( res );
+ cachedElement.setModifications();
+
+ return getCachedComplexElement();
+ }
+
+ public ComplexElement addComplexElement( Residue res, Modification mod )
+ {
+ // first we need a DefaultElement to be dealing withh
+ if( cachedElement == null ){
+ cachedElement = new DefaultComplexElement();
+ }
+
+ // now set this modification so that it looks like the one that we
+ // want.
+ cachedElement.setResidue( res );
+ cachedElement.setModifications( mod );
+
+ return getCachedComplexElement();
+ }
+
+ public ComplexElement addComplexElement( ComplexElement elem, Modification mod )
+ {
+ // do we need a new element
+ if( cachedElement == null ){
+ cachedElement = new DefaultComplexElement();
+ }
+
+ // we now want to set the Modification up to duplicate the old one
+ // (PENDING) I think that there is a problem here. Really this
+ // method should work whether for all objects of type
+ // ComplexElement. The problem is at the moment I havent
+ // adequately defined the notion of equality of two
+ // ComplexElements. Its not clear for instance whether two
+ // ComplexElements of different classes, but which contain
+ // indentical Residues and Modifications, should be equal.
+
+ cachedElement.setResidue( elem.getResidue() );
+ cachedElement.setModifications( elem.getModifications(), mod );
+
+ // now return the cached copy if it exists, or the one we have
+ // just created.
+ return getCachedComplexElement();
+ }
+
+ public ComplexElement removeComplexElement( ComplexElement elem, Modification mod )
+ {
+ if( cachedElement == null ){
+ cachedElement = new DefaultComplexElement();
+ }
+
+ Modification[] mods = elem.getModifications();
+
+ Modification[] lesserMods = new Modification[ mods.length - 1 ];
+
+ ArrayManipulation.removeFromArray( mods, lesserMods, mod );
+
+ cachedElement.setResidue( elem.getResidue() );
+ cachedElement.setModifications( lesserMods );
+
+ return getCachedComplexElement();
+ }
+
+ private ComplexElement getCachedComplexElement()
+ {
+ // See whether we already have this complex element???
+ Object retnRef = complexElements.get( cachedElement );
+
+
+ if( retnRef != null ){
+ // we have pulled out a weak reference from the hash table which
+ // probably means that we already have an appropriate
+ // element. So we want to retrieve that
+ Object retnObj = ((WeakReference)retnRef).get();
+
+ // we know that when we pulled this reference out of the hash it
+ // would not have returned null (because the referened object is
+ // also refered to by the key. However a GC could have happened
+ // between the get and here. So check for null
+ if( retnObj != null ){
+ return (ComplexElement)retnObj;
+ }
+ }
+
+ // we dont already have this element, so store the one we have
+ // created and return that, make sure that we null the internal we
+ // are storing in this class so that we dont use it next time. We
+ // store it as the valued keyed on itself, so that we can retrieve
+ // this ComplexElement. The point of all this is that
+ // ComplexElements which are .equals() to each other should also
+ // therefore be == to each other outside of this package.
+ complexElements.put( cachedElement, new WeakReference( cachedElement ) );
+ ComplexElement retn = cachedElement;
+ cachedElement = null;
+ return retn;
+ }
+} // WeakComplexElementFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: WeakComplexElementFactory.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/03/01 14:33:08 lord
+ * Initial checkin
+ *
+ * Revision 1.1 2000/02/29 11:24:57 lord
+ * Initial Checkin
+ *
+ */
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.java b/src/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.java
new file mode 100644
index 0000000..258883f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/WeakModificationSetFactory.java
@@ -0,0 +1,136 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.complex; // Package name inserted by JPack
+import java.lang.ref.WeakReference;
+import java.util.WeakHashMap;
+
+
+/**
+ * WeakModificationSetFactory.java
+ *
+ *
+ * Created: Wed Mar 1 15:09:49 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: WeakModificationSetFactory.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class WeakModificationSetFactory implements ModificationSetFactoryInterface
+{
+
+ private ModificationSet cachedSet;
+ private WeakHashMap modificationSet = new WeakHashMap();
+
+ public ModificationSet getModificationSet()
+ {
+ if( cachedSet == null ){
+ cachedSet = new ModificationSet();
+ }
+
+ cachedSet.setModification();
+ return getCachedModificationSet();
+ }
+
+ public ModificationSet getModificationSet(Modification modification )
+ {
+ if( cachedSet == null ){
+ cachedSet = new ModificationSet();
+ }
+
+ cachedSet.setModification( modification );
+ return getCachedModificationSet();
+ }
+
+ public ModificationSet getModificationSet(Modification[] modifications )
+ {
+ if( cachedSet == null ){
+ cachedSet = new ModificationSet();
+ }
+
+ cachedSet.setModification( modifications );
+ return getCachedModificationSet();
+ }
+
+ public ModificationSet getModificationSet(Modification[] modifications, Modification modification )
+ {
+ // make an array which is big enough.
+ int size = modifications.length;
+ Modification[] longModifications = new Modification[ size + 1 ];
+ // copy the old array across
+ System.arraycopy( modifications, 0, longModifications, 0, size );
+ // and stuff the new one in at then end
+ longModifications[ size ] = modification;
+
+ return getModificationSet( longModifications );
+ }
+
+ private ModificationSet getCachedModificationSet()
+ {
+ // get back the weak reference if it is there
+ Object retnRef = modificationSet.get( cachedSet ) ;
+
+
+ if( retnRef != null ){
+ // we have a weak reference, get what it refers to
+ Object retnObj = ((WeakReference)retnRef).get();
+
+ // check for null again because its possible that the weakly
+ // refered object has been gc'd between the get call and now
+ if( retnObj != null ){
+ return (ModificationSet)retnObj;
+ }
+ }
+
+ // we dont already have this element so we store the one we have
+ // created, null the cachedReference so that we dont use it again,
+ // and then return it
+ modificationSet.put( cachedSet, new WeakReference( cachedSet ) );
+ ModificationSet retn = cachedSet;
+ cachedSet = null;
+ return retn;
+ }
+
+} // WeakModificationSetFactory
+
+
+
+/*
+ * ChangeLog
+ * $Log: WeakModificationSetFactory.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:14:02 lord
+ * Realised that I had not implemented the ComplexSequence. Have now done
+ * this and have made quite a few changes to this package as a result
+ *
+ * Revision 1.1 2000/03/01 20:17:55 lord
+ * Lots of changes
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/complex/package.html b/src/uk/ac/man/bioinf/sequence/complex/package.html
new file mode 100644
index 0000000..cafaff2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/complex/package.html
@@ -0,0 +1,13 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html>
+ <head>
+ <title>uk.ac.man.bioinf.sequence.complex</title>
+ </head>
+
+ <body>
+ Provides complex sequence support. Complex sequences are those
+ sequences which are mostly one kind of sequence, but not quite! An
+ example would be a DNA sequence carrying information about
+ methylation status with it.
+ </body>
+</html>
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/sequence/event/SequenceEvent.java b/src/uk/ac/man/bioinf/sequence/event/SequenceEvent.java
new file mode 100644
index 0000000..5154e6b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/SequenceEvent.java
@@ -0,0 +1,132 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+ /*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+
+/**
+ * SequenceEvent.java
+ *
+ * Instances of this class represent an event to a sequence. It
+ * includes reference to the location of the event, as well as
+ * its type.
+ *
+ * Created: Tue Feb 15 19:12:00 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceEvent.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceEvent extends java.util.EventObject
+{
+
+ private int start; // the start location of the event
+ private int length; // the length of this event
+ private SequenceEventType type; // the type of event (an enum model)
+
+ /**
+ * Constructor to set the event source, location and type.
+ * @param src the source of the event (i.e: the sequence)
+ * @param location the location of the event
+ * @param type the sequence event type
+ */
+ public SequenceEvent(Object src, int location, SequenceEventType type)
+ {
+ super(src); // set the source of the event by calling the parent
+ this.start = location;
+ this.length = 1;
+ this.type = type;
+ }
+
+ /**
+ * Constructor to set the event source, location and type, which allows
+ * the definition of the start and end of an event.
+ * @param src the source of the event (i.e: the sequence)
+ * @param start the start location of the event
+ * @param end the end location of the event
+ * @param type the sequence event type
+ */
+ public SequenceEvent(Object src, int start, int length, SequenceEventType type)
+ {
+ super(src); // set the source of the event by calling the parent
+ this.start = start;
+ this.length = length;
+ this.type = type;
+ }
+
+ /**
+ * Returns the start location of the event.
+ * @return the start
+ */
+ public int getStart()
+ {
+ return this.start;
+ }
+
+ /**
+ * Returns the end location of the event.
+ * @return the end
+ */
+ public int getLength()
+ {
+ return this.length;
+ }
+
+ /**
+ * Returns the seqyence event type.
+ * @return the sequence event type
+ */
+ public SequenceEventType getType()
+ {
+ return this.type;
+ }
+
+ public String toString()
+ {
+ return super.toString() + " of type " + getType() + " @ " + getStart() + " for " + getLength();
+ }
+} // SequenceEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceEvent.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.2 2000/03/01 14:32:27 lord
+ * cosmetic
+ *
+ * Revision 1.1 2000/02/26 18:28:44 jns
+ * Initial coding of file
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.java b/src/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.java
new file mode 100644
index 0000000..1e6c4f5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/SequenceEventProvider.java
@@ -0,0 +1,90 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+
+
+/**
+ * SequenceEventProvider.java
+ *
+ * An interface designed to enforce the methods necessary to listen to a
+ * sequence.
+ *
+ * Created: Thu Mar 2 18:22:26 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceEventProvider.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceEventProvider
+{
+ /**
+ * Adds the specified sequence listener.
+ *
+ * @param listener the sequence listener
+ */
+ public void addSequenceListener(SequenceListener listener);
+
+ /**
+ * Removes the specified sequence listener.
+ *
+ * @param listener the sequence listener
+ */
+ public void removeSequenceListener(SequenceListener listener);
+
+ /**
+ * Adds the specified vetoable sequence listener.
+ *
+ * @param listener the vetoable sequence listener
+ */
+ public void addVetoableSequenceListener(VetoableSequenceListener listener);
+
+ /**
+ * Removes the specified vetoable sequence listener.
+ *
+ * @param listener the vetoable sequence listener
+ */
+ public void removeVetoableSequenceListener(VetoableSequenceListener listener);
+
+}// SequenceEventProvider
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceEventProvider.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/02 18:34:43 jns
+ * initial code. Generated from the code of MutableSequence, which has now
+ * become a marker class.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/event/SequenceEventType.java b/src/uk/ac/man/bioinf/sequence/event/SequenceEventType.java
new file mode 100644
index 0000000..1dd4d73
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/SequenceEventType.java
@@ -0,0 +1,82 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+import uk.ac.man.bioinf.util.AbstractEnumeration;
+
+
+/**
+ * SequenceEventType.java
+ *
+ * This class provides an enumerated type for the SequenceEvent class
+ * to pass around as an identifier
+ *
+ * Created: Tue Feb 15 20:10:48 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceEventType.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public final class SequenceEventType extends AbstractEnumeration
+{
+ private SequenceEventType( String toString )
+ {
+ super( toString );
+ }
+
+ //EventTypes
+ /**
+ * Indicates a insertion event
+ */
+ public static final SequenceEventType INSERT = new SequenceEventType( "Insertion" );
+ public static final SequenceEventType DELETE = new SequenceEventType( "Deletion" );
+ public static final SequenceEventType SET = new SequenceEventType( "Set" );
+ public static final SequenceEventType GAPINSERT = new SequenceEventType( "GapInsert" );
+ public static final SequenceEventType GAPDELETE = new SequenceEventType( "GapDelete" );
+ public static final SequenceEventType UNSPECIFIED = new SequenceEventType( "Unspecified change" );
+} // SequenceEventType
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceEventType.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/06/27 16:08:44 lord
+ * Added generic "Unspecified" category of event
+ *
+ * Revision 1.2 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/02/26 18:28:44 jns
+ * Initial coding of file
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/event/SequenceListener.java b/src/uk/ac/man/bioinf/sequence/event/SequenceListener.java
new file mode 100644
index 0000000..eed1fdb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/SequenceListener.java
@@ -0,0 +1,66 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+import java.util.EventListener;
+
+
+/**
+ * SequenceListener.java
+ *
+ * Listens for events occuring to a sequence
+ * @see SequenceVetoListener
+ *
+ * Created: Tue Feb 15 18:24:38 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceListener.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceListener extends EventListener
+{
+ /**
+ * Method called when a change occurs
+ * @param event
+ */
+ public void changeOccurred( SequenceEvent event );
+}// SequenceListener
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceListener.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/02/26 18:28:44 jns
+ * Initial coding of file
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.java b/src/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.java
new file mode 100644
index 0000000..b28f9c4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/SequenceListenerSupport.java
@@ -0,0 +1,183 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+import java.util.Vector;
+import java.util.Enumeration;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+
+
+/**
+ * SequenceListenerSupport.java
+ *
+ * This class provides support and handles the listeners to a specific
+ * sequence. This ofcourse means there is one support object for one
+ * sequence object.
+ * @see AbstractSequence
+ *
+ * Created: Wed Feb 16 19:28:44 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceListenerSupport.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceListenerSupport
+{
+ private Vector listeners, vetoableListeners;
+
+ public SequenceListenerSupport()
+ {
+ listeners = new Vector();
+ vetoableListeners = new Vector();
+ }
+
+ /**
+ * There is really no point in making an event object if there are
+ * no listeners. This method allows other classes to be intelligent
+ * about the way it does things.
+ * @return a <code>boolean</code> value
+ */
+ public boolean hasListeners()
+ {
+ return (listeners.size() > 0 || vetoableListeners.size() > 0);
+ }
+
+ /**
+ * This function fires the sequence event to all the interested listeners.
+ * It also fires to the vetoable listeners, which are stored separately,
+ * because the interface for VetoableSequenceListener extends the
+ * SequenceListener interface.
+ * @see VetoableSequenceListener
+ * @see SequenceListener
+ *
+ * @param event the event to be fired
+ */
+ public void fireSequenceEvent(SequenceEvent event)
+ {
+ // enumerate through the listeners and exec the changeOccured function
+ for (Enumeration i = listeners.elements(); i.hasMoreElements(); ) {
+ ((SequenceListener)i.nextElement()).changeOccurred(event);
+ }
+ // also enumerate through the vetoable listeners
+ // NB: VetoableSequenceListener extends SequenceListener
+ for (Enumeration i = vetoableListeners.elements(); i.hasMoreElements(); ) {
+ //System.out.println( "Next element is " + i.nextElement() );
+ ((SequenceListener)i.nextElement()).changeOccurred(event);
+ }
+ }
+
+ /**
+ * This function fires the vetoable event to the vetoable listeners.
+ *
+ * @param event the event to be fired
+ */
+ public void fireVetoableSequenceEvent(VetoableSequenceEvent event)
+ throws SequenceVetoException
+ {
+ // enumerate through vetoable listeners only
+ for (Enumeration i = vetoableListeners.elements(); i.hasMoreElements(); ) {
+ ((VetoableSequenceListener)i.nextElement()).vetoableChangeOccurred(event);
+ }
+ }
+
+ /**
+ * Adds a sequence listener object to a Vector of listeners.
+ *
+ * @param listener the sequence listener
+ */
+ public void addSequenceListener(SequenceListener listener)
+ {
+ if( listener == null )
+ throw new NullPointerException( "Can not add null sequence listener" );
+
+ if (listeners.contains(listener)) return;
+ else listeners.addElement(listener);
+ }
+
+ /**
+ * Removes a sequence listener.
+ *
+ * @param listener the sequence listener
+ */
+ public void removeSequenceListener(SequenceListener listener)
+ {
+ listeners.removeElement(listener);
+ }
+
+ /**
+ * Adds a vetoable sequence listener to the Vector of listeners.
+ *
+ * @param listener the vetoable sequence listener
+ */
+ public void addVetoableSequenceListener(VetoableSequenceListener listener)
+ {
+ if( listener == null )
+ throw new NullPointerException( "Can not add null sequence listener" );
+
+ if (vetoableListeners.contains(listener)) return;
+ else vetoableListeners.addElement(listener);
+ addSequenceListener( listener );
+ }
+
+ /**
+ * Removes a vetoable sequence listener.
+ *
+ * @param listener the vetoable sequence listener
+ */
+ public void removeVetoableSequenceListener(VetoableSequenceListener listener)
+ {
+ vetoableListeners.removeElement(listener);
+ removeSequenceListener( listener );
+ }
+} // SequenceListenerSupport
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceListenerSupport.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/09/15 17:06:17 lord
+ * Now has a "hasListeners" method. The point behind this is that it
+ * allows some serious performance speed ups. Classes using this class
+ * were having to open create events even when there were no listeners.
+ *
+ * Revision 1.3 2000/06/27 16:09:49 lord
+ * Null pointer checks in add/remove listener methods. This means that I
+ * do not have to do the same check in the fire event methods
+ *
+ * Revision 1.2 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/02/26 18:28:44 jns
+ * Initial coding of file
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/event/SequenceVetoException.java b/src/uk/ac/man/bioinf/sequence/event/SequenceVetoException.java
new file mode 100644
index 0000000..ef85567
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/SequenceVetoException.java
@@ -0,0 +1,85 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+
+
+/**
+ * SequenceVetoException.java
+ *
+ * An exception thrown when an object vetos a sequence change event.
+ *
+ * Created: Tue Feb 15 21:08:31 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceVetoException.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceVetoException extends Exception
+{
+ private SequenceEvent event;
+
+ /**
+ * The constructor; storing the event as well as source
+ */
+ public SequenceVetoException( String message, SequenceEvent event )
+ {
+ super( message );
+ this.event = event;
+ }
+
+ /**
+ * Returns the sequence event that the veto objected to
+ * @return the sequence event
+ */
+ public SequenceEvent getEvent()
+ {
+ return event;
+ }
+} // SequenceVetoException
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceVetoException.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/09 16:42:13 lord
+ * Package update
+ *
+ * Revision 1.2 2000/02/26 18:43:36 jns
+ * wrong package name for SequenceEvent corrected.
+ *
+ * Revision 1.1 2000/02/26 18:28:45 jns
+ * Initial coding of file
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.java b/src/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.java
new file mode 100644
index 0000000..3578255
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/VetoableSequenceEvent.java
@@ -0,0 +1,72 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+
+/**
+ * VetoableSequenceEvent.java
+ *
+ *
+ * Created: Fri Feb 18 17:38:50 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: VetoableSequenceEvent.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class VetoableSequenceEvent extends SequenceEvent
+{
+
+ public VetoableSequenceEvent( Object src, int location, SequenceEventType type )
+ {
+ super( src, location, type );
+ }
+
+ public VetoableSequenceEvent( Object src, int start, int length, SequenceEventType type )
+ {
+ super( src, start, length, type );
+ }
+
+} // VetoableSequenceEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: VetoableSequenceEvent.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/02/26 18:28:45 jns
+ * Initial coding of file
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.java b/src/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.java
new file mode 100644
index 0000000..10e7e76
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/event/VetoableSequenceListener.java
@@ -0,0 +1,73 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.sequence.event; // Package name inserted by JPack
+
+/**
+ * VetoableSequenceListener.java
+ *
+ * When a sequence wishes to change it should signal listeners of this
+ * type first before it makes the change. If none of these listeners
+ * veto the change, then it make occur after which listeners to type
+ * SequenceChangeListener (including all of the
+ * VetoableSequenceListeners ) should be signalled, at which
+ * stage the change is unvetoable. Because there are two types of
+ * listener it is not necessary to resignal the
+ * VetoableSequenceListener's if a change is latter veto'd
+ *
+ * Created: Tue Feb 15 19:28:56 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: VetoableSequenceListener.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface VetoableSequenceListener extends SequenceListener
+{
+ /**
+ * Method signalled before a prospective change occurs
+ * @param event the event
+ * @exception SequenceVetoException if the listener does not wish
+ * the event to occur.
+ */
+ public void vetoableChangeOccurred( VetoableSequenceEvent event )
+ throws SequenceVetoException;
+
+}// VetoableSequenceListener
+
+
+/*
+ * ChangeLog
+ * $Log: VetoableSequenceListener.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/06/27 16:10:55 lord
+ * Removed backtick from the comments. The new sentance is now
+ * ungrammatical but does not confuse Emacs' sexp matching algorithm
+ *
+ * Revision 1.2 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/02/26 18:28:45 jns
+ * Initial coding of file
+ *
+ *
+ */
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.java b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.java
new file mode 100644
index 0000000..697808f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentDimension.java
@@ -0,0 +1,169 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.geom; // Package name inserted by JPack
+
+
+/**
+ * SequenceAlignmentDimension.java
+ *
+ * Represents a dimension within a SA. It is not a vast amount of use
+ * without a point of reference (SequenceAlignmentPoint).
+ * @see SequenceAlignmentPoint
+ *
+ * Created: Mon Mar 27 12:01:25 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceAlignmentDimension.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceAlignmentDimension
+{
+ private int width, height;
+
+ public SequenceAlignmentDimension()
+ {
+ // generate a dimension of width=1, and height=1
+ setSize(1, 1);
+ }
+
+ public SequenceAlignmentDimension(int w, int h)
+ {
+ setSize(w, h);
+ }
+
+ public SequenceAlignmentDimension(SequenceAlignmentDimension dim)
+ {
+ setSize(dim);
+ }
+
+ /**
+ * Ascertains the equality of a given dimension to this
+ * object. Overrides the method in Object.
+ *
+ * @param obj the dimension
+ * @return the equality of the objects
+ */
+ public boolean equals(Object obj)
+ {
+ /*
+ * if the object is an instance of SADimension, and the width and
+ * heights are equal, then the objects are said to be equivelent.
+ */
+ if ((obj instanceof SequenceAlignmentDimension) &&
+ ((((SequenceAlignmentDimension)obj).getWidth() == this.width) &&
+ (((SequenceAlignmentDimension)obj).getHeight() == this.height)))
+ return true;
+ else
+ return false;
+ }
+
+ /**
+ * Sets the size of the dimension. This method may further be
+ * expanded if listeneers are appropriate, and to include any
+ * necessary error checking.
+ *
+ * @param w the width of the dimension
+ * @param h the height of the dimension
+ */
+ public void setSize(int w, int h)
+ {
+ this.width = w;
+ this.height = h;
+ }
+
+ /**
+ * Sets the size of the dimension. This method will allow a
+ * dimension to be duplicated. Calls setSize(int, int) to save on
+ * correction procedures.
+ *
+ * @param dim a value of type 'SequenceAlignmentDimension'
+ */
+ public void setSize(SequenceAlignmentDimension dim)
+ {
+ // calls setDimension(int, int) to enable corrections to the
+ // procedure to be made in one place
+ setSize(dim.getWidth(), dim.getHeight());
+ }
+
+ /**
+ * Allows the resize of the dimension
+ *
+ * @param w the new width of the dimension
+ * @param h the new height of the dimension
+ */
+ public void resize(int w, int h)
+ {
+ setSize(w, h);
+ }
+
+ /**
+ * Returns the dimensions of this dimension (que????).
+ *
+ * @return the SA dimension
+ */
+ public SequenceAlignmentDimension getSize()
+ {
+ // returning a new SAD to avoid problems of SAD being altered at a
+ // later stage
+ return new SequenceAlignmentDimension
+ (this.width, this.height);
+ }
+
+ /**
+ * Returns the width of this dimension.
+ *
+ * @return the width
+ */
+ public int getWidth()
+ {
+ return this.width;
+ }
+
+ /**
+ * Returns the height of this dimension.
+ *
+ * @return the height
+ */
+ public int getHeight()
+ {
+ return this.height;
+ }
+} // SequenceAlignmentDimension
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignmentDimension.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/27 11:27:57 jns
+ * o initial coding of a sequence alignment dimension.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.java b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.java
new file mode 100644
index 0000000..848058b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentPoint.java
@@ -0,0 +1,250 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.geom; // Package name inserted by JPack
+
+
+/**
+ * SequenceAlignmentPoint.java
+ *
+ * Represents a point in an alignment, where X is the position in a
+ * sequence, and Y is the index of the sequence in the alignment. No
+ * checking is currently written into this object for the validity of
+ * the point, and the opportunity to use listeners is not seized
+ * (although this can easily be added later).
+ *
+ * Created: Mon Mar 27 11:16:19 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceAlignmentPoint.java,v 1.9 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceAlignmentPoint implements Cloneable, Comparable
+{
+ private int x, y;
+
+ public SequenceAlignmentPoint()
+ {
+ // create a point at (1,1)
+ setLocation(1, 1);
+ }
+
+ public SequenceAlignmentPoint(int x, int y)
+ {
+ setLocation(x, y);
+ }
+
+ public SequenceAlignmentPoint(SequenceAlignmentPoint point)
+ {
+ setLocation(point);
+ }
+
+ /**
+ * Ascertains the equality of a given point to this
+ * object. Overrides the method in Object.
+ *
+ * @param obj the point
+ * @return the equality of the objects
+ */
+ public boolean equals(Object obj)
+ {
+ /*
+ * if the object is an instance of SAPoint, and the coordinates
+ * are equal, then the objects are equivelent; otherwise they are
+ * considered not to be equal.
+ */
+ if ( obj instanceof SequenceAlignmentPoint &&
+ ((SequenceAlignmentPoint)obj).x == this.x &&
+ ((SequenceAlignmentPoint)obj).y == this.y )
+ return true;
+ else
+ return false;
+ }
+
+ /**
+ * Compares this point to another. Points are compared by comparing
+ * first the value of getX(), and then getY(). If obj is not a
+ * SequenceAlignmentPoint an exception is thrown.
+ */
+ public int compareTo( Object obj )
+ {
+ SequenceAlignmentPoint point = (SequenceAlignmentPoint)obj;
+
+ // compare X
+ if( x > point.x ){
+ return 1;
+ }
+ else if ( x < point.x ){
+ return -1;
+ }
+ // so x is equal. Now compare y
+ else if ( y > point.y ){
+ return 1;
+ }
+ else if( y < point.y ){
+ return -1;
+ }
+
+ // we are equal
+ return 0;
+ }
+
+
+ public SequenceAlignmentPoint setX( int x )
+ {
+ this.x = x;
+ return this;
+ }
+
+ public SequenceAlignmentPoint setY( int y )
+ {
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * Sets the location of the point. This method can be further
+ * expanded if listeners are appropriate, and to include error
+ * checking.
+ *
+ * @param x the x position of the point
+ * @param y the y position of the point
+ */
+ public SequenceAlignmentPoint setLocation(int x, int y)
+ {
+ this.x = x;
+ this.y = y;
+ return this;
+ }
+
+ /**
+ * Sets the location of the point. This method will allow a point to
+ * be duplicated. Calls setLocation(int, int) to save on correction
+ * procedures.
+ *
+ * @param point the point in a sequence alignment
+ */
+ public SequenceAlignmentPoint setLocation(SequenceAlignmentPoint point)
+ {
+ // calls setLocation(int, int) to enable corrections to the
+ // procedure to be made in one place
+ return setLocation(point.getX(), point.getY());
+ }
+
+ /**
+ * Allows the moving of a point to a new position.
+ *
+ * @param x the X index
+ * @param y the Y index
+ */
+ public SequenceAlignmentPoint move(int x, int y)
+ {
+ return setLocation(x, y);
+ }
+
+ /**
+ * Returns the location in the sequence alignment, represented by
+ * this object.
+ *
+ * @return the location represented by this point
+ */
+ public SequenceAlignmentPoint getLocation()
+ {
+ // returns a new SAP to avoid problems with the SAP altering at a
+ // later date
+ return new SequenceAlignmentPoint
+ (this.x, this.y);
+ }
+
+ /**
+ * Returns the X index of the point.
+ *
+ * @return the X index
+ */
+ public int getX()
+ {
+ return this.x;
+ }
+
+ /**
+ * Returns the Y index of the point.
+ *
+ * @return the Y index
+ */
+ public int getY()
+ {
+ return this.y;
+ }
+
+ public Object clone() throws CloneNotSupportedException
+ {
+ return super.clone();
+ }
+
+ public String toString()
+ {
+ return "SequenceAlignmentPoint at ( " + x + ", " + y + " )";
+ }
+} // SequenceAlignmentPoint
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignmentPoint.java,v $
+ * Revision 1.9 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.8 2001/01/23 17:58:00 lord
+ * Support for comparable interface
+ *
+ * Revision 1.7 2001/01/19 19:50:37 lord
+ * Some new accessor methods
+ *
+ * Revision 1.6 2000/04/06 15:45:32 lord
+ * A few changes to speed up the equals method
+ *
+ * Revision 1.5 2000/04/05 14:26:34 lord
+ * Added toString, and clone
+ *
+ * Revision 1.4 2000/04/04 17:48:03 lord
+ * Now clonable
+ *
+ * Revision 1.3 2000/03/29 15:39:53 lord
+ * Moved default location to 1,1 rather than 0,0 as the latter
+ * isnt valid!
+ *
+ * Revision 1.2 2000/03/27 11:19:38 jns
+ * altering getLocation() to make thread safe.
+ *
+ * Revision 1.1 2000/03/27 10:57:35 jns
+ * o initial coding of a SA point [based on a java.awt.point].
+ *
+ */
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.java b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.java
new file mode 100644
index 0000000..a888b51
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentRectangle.java
@@ -0,0 +1,379 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.geom; // Package name inserted by JPack
+
+
+/**
+ * SequenceAlignmentRectangle.java
+ *
+ * Defines a rectangular region in a sequence alignment. NB: objects
+ * of this class perform no checks as to the validity of the region
+ * defined.
+ *
+ * Created: Mon Mar 27 12:41:18 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceAlignmentRectangle.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceAlignmentRectangle implements SequenceAlignmentShape, Comparable
+{
+ private SequenceAlignmentPoint location;
+ private SequenceAlignmentDimension size;
+
+ public SequenceAlignmentRectangle()
+ {
+ this( 1, 1, 1, 1 );
+ }
+
+ public SequenceAlignmentRectangle(int x, int y, int width, int height)
+ {
+ setBounds(x, y, width, height);
+ }
+
+ public SequenceAlignmentRectangle(SequenceAlignmentRectangle rect)
+ {
+ setBounds(rect);
+ }
+
+ public SequenceAlignmentRectangle
+ (int x, int y, SequenceAlignmentDimension dim)
+ {
+ setBounds(x, y, dim.getWidth(), dim.getHeight());
+ }
+
+ public SequenceAlignmentRectangle
+ (SequenceAlignmentPoint point, int width, int height)
+ {
+ setBounds(point.getX(), point.getY(), width, height);
+ }
+
+ /**
+ * Determines whether a point is contained in this region.
+ *
+ * @param x the position in the sequence
+ * @param y the sequence index in the alignment
+ * @return whether a point is contained in this region
+ */
+ public boolean contains(int x, int y)
+ {
+ /*
+ * if x and y are greater than the corresponding location to this
+ * rectangle, but less than the corresponding location +
+ * dimension, then the point is contained within this rectangle.
+ * The - 1's are because a SARhas a size of at least 1
+ */
+ if (((x >= this.location.getX()) && (y >= this.location.getY())) &&
+ ((x <= (this.location.getX() + this.size.getWidth() - 1 )) &&
+ (y <= (this.location.getY() + this.size.getHeight() - 1 )))){
+ return true;
+ }
+ else{
+ return false;
+ }
+ }
+
+ /**
+ * Determines whether a point is contained in this region.
+ *
+ * @param point the point
+ * @return whether a point is contained in this region
+ */
+ public boolean contains(SequenceAlignmentPoint point)
+ {
+ /*
+ * Delegates to the method contains(int, int) to allow easy update
+ * of the procedure
+ */
+ return contains(point.getX(), point.getY());
+ }
+
+ /**
+ * Compares two SARectangles for equality (ie: whether they have the
+ * same dimension and location).
+ *
+ * @param obj the SARectangle for comparison
+ * @return the equality of the objects
+ */
+ public boolean equals(Object obj)
+ {
+ /*
+ * if the object is an instance of SARectangle, and the point and
+ * dimensions are equal, then the objects are said to be
+ * equivelent.
+ */
+ if ((obj instanceof SequenceAlignmentRectangle) &&
+ ((((SequenceAlignmentRectangle)obj).getLocation().equals(this.location)) &&
+ (((SequenceAlignmentRectangle)obj).getSize().equals(this.size))))
+ return true;
+ else
+ return false;
+ }
+
+ /**
+ * Compares another rectangle to this one. Comparison is done by
+ * comparing the location point. If this is equal then the width,
+ * then the height are compared. Throws a class cast if obj is
+ * not a SequenceAlignmentRectangle
+ */
+ public int compareTo( Object obj )
+ {
+ SequenceAlignmentRectangle rect = (SequenceAlignmentRectangle)obj;
+
+ // get rid of the equals case first.
+ if( equals( rect ) ) return 0;
+
+ // now compare locations
+ int comp = location.compareTo( rect.location );
+
+ if( comp != 0 ) return comp;
+
+ // so locations are the same, compare width, and then height
+ if( size.getWidth() < rect.size.getWidth() ){
+ return -1;
+ } else if( size.getHeight() < rect.size.getHeight() ){
+ return -1;
+ }
+
+ return 1;
+ }
+
+
+ /**
+ * Sets the boundry defined by this region.
+ *
+ * @param x the position in the sequence
+ * @param y the sequence index in the alignment
+ * @param width the width of the SARectangle
+ * @param height the height of the SARectangle
+ */
+ public void setBounds(int x, int y, int width, int height)
+ {
+ this.location = new SequenceAlignmentPoint(x, y);
+ this.size = new SequenceAlignmentDimension(width, height);
+ }
+
+ /**
+ * Sets the boundry defined by this region.
+ *
+ * @param point the origin location of the new SARectangle
+ * @param dim the size of the new SARectangle
+ */
+ public void setBounds
+ (SequenceAlignmentPoint point, SequenceAlignmentDimension dim)
+ {
+ /*
+ * Delegates action to setBounds(int, int, int, int) to enable
+ * easy update of procedures
+ */
+ setBounds(point.getX(), point.getY(), dim.getWidth(), dim.getHeight());
+ }
+
+ /**
+ * Sets the boundry defined by this region.
+ *
+ * @param rect the rectangle
+ */
+ public void setBounds(SequenceAlignmentRectangle rect)
+ {
+ /*
+ * Delegates action to setBounds(int, int, int, int) to enable
+ * easy update of procedures
+ */
+ setBounds(rect.getLocation().getX(), rect.getLocation().getY(),
+ rect.getSize().getWidth(), rect.getSize().getHeight());
+ }
+
+ /**
+ * Returns the rectangle which defines the boundries of the region
+ * defined by this object.
+ * @see SequenceAlignmentShape
+ *
+ * @return the rectangle
+ */
+ public SequenceAlignmentRectangle getBounds() // from SequenceAlignmentShape
+ {
+ return new SequenceAlignmentRectangle(this);
+ }
+
+ /**
+ * Sets the progom location of the rectangle. X corresponds to the
+ * position in the sequence, and Y corresponds to the index of the
+ * sequence in the alignment.
+ *
+ * @param x the new X location of the rectangle
+ * @param y the new Y location of the rectangle
+ */
+ public void setLocation(int x, int y)
+ {
+ this.location = new SequenceAlignmentPoint(x, y);
+ }
+
+ /**
+ * Sets the origin location of the rectangle.
+ *
+ * @param point the new location
+ */
+ public void setLocation(SequenceAlignmentPoint point)
+ {
+ /*
+ * Delegates action to setLocation(int, int) so that if
+ * modifications to code are necessary, they can be made in one
+ * place.
+ */
+ setLocation(point.getX(), point.getY());
+ }
+
+ /**
+ * Returns the location of the rectangle
+ *
+ * @return the location
+ */
+ public SequenceAlignmentPoint getLocation()
+ {
+ return new SequenceAlignmentPoint(this.location);
+ }
+
+ /**
+ * Sets the size of the rectangle.
+ *
+ * @param width the width of the new rectangle
+ * @param height the height of the new rectangle
+ */
+ public void setSize(int width, int height)
+ {
+ this.size = new SequenceAlignmentDimension(width, height);
+ }
+
+ /**
+ * Sets the size of the rectangle.
+ *
+ * @param dim the new dimension
+ */
+ public void setSize(SequenceAlignmentDimension dim)
+ {
+ /*
+ * Delegates action to setSize(int, int) so that if modifications
+ * to code are necessary, they can be made in one place.
+ */
+ setSize(dim.getWidth(), dim.getHeight());
+ }
+
+ /**
+ * Returns the size of the rectangle.
+ *
+ * @return the dimensions of the rectangle
+ */
+ public SequenceAlignmentDimension getSize()
+ {
+ return new SequenceAlignmentDimension(this.size);
+ }
+
+ public int getX()
+ {
+ return location.getX();
+ }
+
+ public int getY()
+ {
+ return location.getY();
+ }
+
+ public int getHeight()
+ {
+ return size.getHeight();
+ }
+
+ public int getWidth()
+ {
+ return size.getWidth();
+ }
+
+ public void add( SequenceAlignmentPoint point )
+ {
+ add( point.getX(), point.getY() );
+ }
+
+ public void add( int newx, int newy )
+ {
+ // this code is culled from java.awt.Rectangle
+ // (PENDING:- PL) Does this not suggest that all of the geom
+ // classes should be re-written to simply wrap the awt geom
+ // classes? Probably.
+ int x = location.getX();
+ int y = location.getY();
+ int width = size.getWidth();
+ int height = size.getHeight();
+
+ // the some what counter intuitive + 1's here are because the
+ // minimum size of a Rectangle is 1, 1...
+ int x1 = Math.min( x, newx );
+ int x2 = Math.max( x + width, newx + 1);
+ int y1 = Math.min( y, newy );
+ int y2 = Math.max( y + height, newy + 1 );
+
+ setLocation( x1, y1 );
+ setSize( (x2 - x1), (y2 - y1) );
+ }
+
+ public String toString()
+ {
+ return super.toString() + " Location [" + location.getX() + "x" + location.getY() +
+ "+" + size.getWidth() + "+" + size.getHeight() + "]";
+ }
+} // SequenceAlignmentRectangle
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignmentRectangle.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/23 17:58:00 lord
+ * Support for comparable interface
+ *
+ * Revision 1.4 2001/01/19 19:50:23 lord
+ * This class now uses exclusive numbers. This makes it behave more
+ * intuitively. At least in some circumstances. In others it makes it
+ * less so.
+ *
+ * Revision 1.3 2000/06/13 11:03:24 lord
+ * Added getX, getY methods
+ *
+ * Revision 1.2 2000/04/13 15:37:19 lord
+ * Added "add" method. Fiddled with "contains" method
+ *
+ * Revision 1.1 2000/03/27 13:29:48 jns
+ * o initial coding of a SA rectangle which may be used to define a region in
+ * a MSA.
+ *
+ */
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.java b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.java
new file mode 100644
index 0000000..d2c18e4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/geom/SequenceAlignmentShape.java
@@ -0,0 +1,64 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.geom; // Package name inserted by JPack
+
+
+/**
+ * SequenceAlignmentShape.java
+ *
+ * Defines a shape used to identify a region in a sequence alignment.
+ *
+ * Created: Mon Mar 27 12:38:04 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceAlignmentShape.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceAlignmentShape
+{
+ /**
+ * Returns the boundaries of the shape used to identify a region in
+ * a sequence alignment.
+ *
+ * @return the rectangle that defines the boundries
+ */
+ public SequenceAlignmentRectangle getBounds();
+}// SequenceAlignmentShape
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignmentShape.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/03/27 13:27:07 jns
+ * o initial coding of a SA shape which can be used to define a shape in a MSA.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.java b/src/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.java
new file mode 100644
index 0000000..4c28c7d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/group/AbstractGappedSequenceGroup.java
@@ -0,0 +1,78 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.group; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+
+/**
+ * AbstractGappedSequenceGroup.java
+ *
+ *
+ * Created: Thu Jun 1 18:25:15 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractGappedSequenceGroup.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractGappedSequenceGroup implements GappedSequenceGroup
+{
+ public AbstractGappedSequenceGroup()
+ {
+ }
+
+ public GappedSequence[] getGappedSequences()
+ {
+ Sequence[] retnSeqs = getSequences();
+ GappedSequence[] retn = new GappedSequence[ retnSeqs.length ];
+ System.arraycopy( retnSeqs, 0, retn, 0, retn.length );
+ return retn;
+ }
+} // AbstractGappedSequenceGroup
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractGappedSequenceGroup.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/06/05 14:46:25 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.java b/src/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.java
new file mode 100644
index 0000000..6badc9e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/group/DefaultGappedSequenceGroup.java
@@ -0,0 +1,137 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.group; // Package name inserted by JPack
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+
+/**
+ * DefaultGappedSequenceGroup.java
+ *
+ *
+ * Created: Thu Jun 1 18:33:14 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DefaultGappedSequenceGroup.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DefaultGappedSequenceGroup extends AbstractGappedSequenceGroup
+{
+ private List sequences = new ArrayList();
+ private GappedSequence[] cache;
+ private boolean cacheOutOfDate = true;
+
+ public DefaultGappedSequenceGroup()
+ {
+ super();
+ }
+
+ public void addSequenceToGroup( Sequence seq )
+ {
+ cacheOutOfDate = true;
+ sequences.add( seq );
+ }
+
+ public void removeSequenceFromGroup( Sequence seq )
+ {
+ cacheOutOfDate = true;
+ sequences.remove( seq );
+ }
+
+ public boolean containsSequence( Sequence seq )
+ {
+ return sequences.contains( seq );
+ }
+
+ public Sequence[] getSequences()
+ {
+ if( cacheOutOfDate ){
+ // must have written this code a 1000 times before.
+ Object[] retnObj = sequences.toArray();
+ cache = new GappedSequence[ retnObj.length ];
+ System.arraycopy( retnObj, 0, cache, 0, cache.length );
+ }
+ return cache;
+ }
+
+ public void clearSequences()
+ {
+ cacheOutOfDate = true;
+ sequences.clear();
+ }
+
+ public int getNumberSequences()
+ {
+ return sequences.size();
+ }
+
+
+ public Sequence getSequenceAt( int index )
+ {
+ return (Sequence)sequences.get( index );
+ }
+
+ public GappedSequence getGappedSequenceAt( int index )
+ {
+ return (GappedSequence)sequences.get( index );
+ }
+
+ public Iterator iterator()
+ {
+ return sequences.iterator();
+ }
+} // DefaultGappedSequenceGroup
+
+
+
+/*
+ * ChangeLog
+ * $Log: DefaultGappedSequenceGroup.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.3 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/06/05 14:46:25 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.java b/src/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.java
new file mode 100644
index 0000000..7fa2167
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/group/GappedSequenceGroup.java
@@ -0,0 +1,67 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.group; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+
+/**
+ * GappedSequenceGroup.java
+ *
+ * An extension of SequenceGroup with some methods to return
+ * GappedSequences.
+ * Created: Thu Jun 1 18:17:54 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GappedSequenceGroup.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface GappedSequenceGroup extends SequenceGroup
+{
+ /**
+ * Return all the sequences in this group as a GappedSequence
+ * array. If this group contains sequences which are not
+ * GappedSequences this will result in a run time
+ * ClassCastException
+ * @return the sequences
+ */
+ public GappedSequence[] getGappedSequences();
+
+}// GappedSequenceGroup
+
+
+/*
+ * ChangeLog
+ * $Log: GappedSequenceGroup.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/06/05 14:46:25 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.java b/src/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.java
new file mode 100644
index 0000000..32b4691
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/group/GroupSequenceAlignment.java
@@ -0,0 +1,406 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.group; // Package name inserted by JPack
+import java.lang.UnsupportedOperationException;
+import java.util.ConcurrentModificationException;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.NoSuchSequenceException;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEventType;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListenerSupport;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceListenerSupport;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.geom.SequenceAlignmentRectangle;
+import uk.ac.man.bioinf.sequence.identifier.Identifier;
+import uk.ac.man.bioinf.util.IntArrayList;
+
+
+/**
+ * GroupSequenceAlignment.java
+ *
+ * This is a sequence group which also reflects a sequence
+ * alignment. The sequences will be given out in the same order, as
+ * they are in the SequenceAlignment. A given group is linked
+ * specifically to a single SequenceAlignment. If sequences are
+ * removed from the SequenceAlignment then they are automatically
+ * removed from this class.
+ *
+ * Created: Thu Jun 1 23:20:37 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GroupSequenceAlignment.java,v 1.9 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class GroupSequenceAlignment extends AbstractGappedSequenceGroup implements SequenceAlignment, AlignmentListener
+{
+ private SequenceAlignment alignment;
+ // this should store the index of the sequence in the sequence
+ // alignment, at the relevant index in this SequenceAlignment
+ private IntArrayList seqArray = new IntArrayList();
+ private int changeNumber = 0;
+ private AlignmentListenerSupport alignSupp = new AlignmentListenerSupport();
+ private SequenceListenerSupport seqSupp = new SequenceListenerSupport();
+
+ /**
+ * Start an empty sequence group associated with the given sequence
+ * alignment.
+ * @param alignment the alignment
+ */
+ public GroupSequenceAlignment( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ alignment.addAlignmentListener( this );
+ alignment.addSequenceListener ( this );
+ }
+
+ /**
+ * Starts an Sequence group with the sequences given in the IntArrayList
+ * @param alignment
+ * @param seqArray
+ */
+ public GroupSequenceAlignment( SequenceAlignment alignment, IntArrayList seqArray )
+ {
+ this( alignment );
+
+ int length = alignment.getNumberSequences();
+ for( int i = 0; i < seqArray.size(); i++ ){
+ int val = seqArray.get( i );
+ if( val < 1 || val > length ){
+ throw new
+ IllegalArgumentException( "The value " + val + " at position " + i + " is outside the allowable range" );
+ }
+ }
+ }
+
+
+ public Sequence[] getSequences()
+ {
+ Sequence[] retn = new Sequence[ seqArray.size() ];
+
+ for( int i = 0; i < retn.length; i++ ){
+ retn[ i ] = alignment.getSequenceAt( seqArray.get( i ) );
+ } //end for( i < retn.length; )
+
+ return retn;
+ }
+
+ /**
+ * Adds a sequence to this group.
+ * @throws IllegalArgumentException if this sequence is not part of
+ * the associated SequenceAlignment
+ * @param sequence the sequence
+ */
+ public void addSequenceToGroup( Sequence sequence )
+ {
+ try{
+ alignSupp.fireVetoableAlignmentEvent
+ ( new VetoableAlignmentEvent( this, seqArray.size(), AlignmentEventType.INSERT ) );
+ }
+ catch( AlignmentVetoException ave ){
+ // (PENDING:- PL) I'm not really sure what I should do at this
+ // point
+ }
+
+ int index = alignment.getSequenceIndex( (GappedSequence)sequence );
+ if( index == -1 )
+ throw new IllegalArgumentException( "The sequence must be a member of the associated sequence alignment" );
+ seqArray.add( index );
+
+ alignSupp.fireAlignmentEvent
+ ( new AlignmentEvent( this, seqArray.size(), AlignmentEventType.INSERT ) );
+
+ changeNumber++;
+ }
+
+ public void addSequence(GappedSequence seq, int inset)
+ throws AlignmentVetoException
+ {
+ /* (PENDING: JNS) 26.10.00 an implementation would be nice when I
+ * understand what this should do in respect of the group.
+ */
+ }
+
+ public int getLength()
+ {
+ return alignment.getLength();
+ }
+
+ public void removeSequenceFromGroup( Sequence sequence )
+ {
+ int index = alignment.getSequenceIndex( (GappedSequence)sequence );
+ if( index != -1 ){
+
+ try{
+ alignSupp.fireVetoableAlignmentEvent
+ ( new VetoableAlignmentEvent( this, index, AlignmentEventType.DELETE ) );
+ }
+ catch( AlignmentVetoException ave ){
+ // (PENDING:- PL) I'm not really sure what to do at this point
+ }
+
+ // may be able to move this to a binary search if I ensure the
+ // array is sorted.
+ seqArray.remove( seqArray.linearSearch( index ) );
+ changeNumber++;
+
+ alignSupp.fireAlignmentEvent
+ ( new AlignmentEvent( this, index, AlignmentEventType.DELETE ) );
+ }
+ }
+
+ public GappedSequence removeSequence(int seqIndex)
+ throws AlignmentVetoException
+ {
+ /* (PENDING: JNS) 26.10.00 an implementation would be nice when I
+ * understand what this should do in respect of the group.
+ */
+ return null;
+ }
+
+ public void setInset(int seqIndex, int size) throws AlignmentVetoException
+ {
+ /* (PENDING: JNS) 26.10.00 an implementation would be nice when I
+ * understand what this should do in respect of the group.
+ */
+ }
+
+ public void clearSequences()
+ {
+ try{
+ alignSupp.fireVetoableAlignmentEvent
+ ( new VetoableAlignmentEvent( this, 1, seqArray.size(), AlignmentEventType.DELETE ) );
+ }
+ catch( AlignmentVetoException sve ){
+ // (PENDING:- PL) Not really sure what to do here
+ }
+
+ seqArray.clear();
+ changeNumber++;
+
+ alignSupp.fireAlignmentEvent
+ ( new AlignmentEvent( this, 1, seqArray.size(), AlignmentEventType.DELETE ) );
+ }
+
+ public int getNumberSequences()
+ {
+ return seqArray.size();
+ }
+
+ public boolean containsSequence( Sequence sequence )
+ {
+ int alignmentIndex = alignment.getSequenceIndex( (GappedSequence)sequence );
+ return ( seqArray.linearSearch( alignmentIndex ) != -1 );
+ }
+
+ public Iterator iterator()
+ {
+ return new Iterator(){
+ private int expectedChangeNumber = changeNumber;
+ private int index = 0;
+ public boolean hasNext()
+ {
+ if( expectedChangeNumber != changeNumber ){
+ throw new ConcurrentModificationException( "GroupSequenceAlignment has been modified" );
+ }
+
+ return( index < getLength() );
+ }
+
+ public Object next()
+ {
+ if( expectedChangeNumber != changeNumber ){
+ throw new ConcurrentModificationException( "GroupSequenceAlignment has been modified" );
+ }
+
+ return alignment.getSequenceAt( seqArray.get( index++ ) );
+ }
+
+ public void remove()
+ {
+ throw new UnsupportedOperationException( "GroupSequenceAlignment does not support the remove method" );
+ }
+ };
+ }
+
+ // sequence alignment interface.
+ public GappedSequence getSequenceAt( int index )
+ {
+ return alignment.getSequenceAt( seqArray.get( index - 1) );
+ }
+
+ public SequenceAlignment getSubAlignment( int startPos, int endPos, int startSeq, int endSeq )
+ {
+ throw new RuntimeException( "Not implemented yet" );
+ }
+
+ public SequenceAlignment getSubAlignment( SequenceAlignmentRectangle rect )
+ {
+ return getSubAlignment( rect.getX(), rect.getWidth(), rect.getY(), rect.getHeight() );
+ }
+ public SequenceType getSequenceType()
+ {
+ return alignment.getSequenceType();
+ }
+
+ public int getInset( int index )
+ {
+ try{
+ return alignment.getInset( seqArray.get( index - 1 ) );
+ }
+ catch( NoSuchElementException nsee ){
+ throw new NoSuchSequenceException( this, index );
+ }
+ }
+
+ public int getSequenceIndex( GappedSequence sequence )
+ {
+ return seqArray.linearSearch( alignment.getSequenceIndex( sequence ) ) + 1;
+ }
+
+ public void removeAlignmentListener( AlignmentListener listener )
+ {
+ alignSupp.removeAlignmentListener( listener );
+ }
+
+ public void addAlignmentListener( AlignmentListener listener )
+ {
+ alignSupp.addAlignmentListener( listener );
+ }
+
+ public void removeVetoableAlignmentListener( VetoableAlignmentListener listener )
+ {
+ alignSupp.removeVetoableAlignmentListener( listener );
+ }
+
+ public void addVetoableAlignmentListener( VetoableAlignmentListener listener )
+ {
+ alignSupp.addVetoableAlignmentListener( listener );
+ }
+
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ if( containsSequence( (Sequence)event.getSource() ) )
+ seqSupp.fireSequenceEvent( event );
+ }
+
+ public void vetoableChangeOccurred( VetoableSequenceEvent event ) throws SequenceVetoException
+ {
+ if( containsSequence( (Sequence)event.getSource() ) )
+ seqSupp.fireVetoableSequenceEvent( event );
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ alignSupp.fireAlignmentEvent( new AlignmentEvent( this, 1, getNumberSequences(),
+ AlignmentEventType.UNSPECIFIED ) );
+ }
+
+ public void vetoableChangeOccurred( VetoableAlignmentEvent event ) throws AlignmentVetoException
+ {
+ alignSupp.fireVetoableAlignmentEvent( new VetoableAlignmentEvent( this, 1, getNumberSequences(),
+ AlignmentEventType.UNSPECIFIED ) );
+ }
+
+ public void addSequenceListener( SequenceListener listener )
+ {
+ seqSupp.addSequenceListener( listener );
+ }
+
+ public void removeSequenceListener( SequenceListener listener )
+ {
+ seqSupp.removeSequenceListener( listener );
+ }
+
+ // this method can safely delegate to the sequence alignment.
+ public void addVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ seqSupp.addVetoableSequenceListener( listener );
+ }
+
+ public void removeVetoableSequenceListener( VetoableSequenceListener listener )
+ {
+ seqSupp.removeVetoableSequenceListener( listener );
+ }
+
+ public Identifier getIdentifier()
+ {
+ return alignment.getIdentifier();
+ }
+} // GroupSequenceAlignment
+
+
+
+/*
+ * ChangeLog
+ * $Log: GroupSequenceAlignment.java,v $
+ * Revision 1.9 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.8 2001/03/12 16:50:21 lord
+ * Now fully supports interface, and sequence change events
+ *
+ * Revision 1.7 2001/01/23 17:59:19 lord
+ * Added getSubAlignment( SequenceAlignmentRectangle ) method because I
+ * thought it would be useful.
+ *
+ * Revision 1.6 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.5 2000/10/19 17:54:25 lord
+ * New constructor added.
+ *
+ * Revision 1.4 2000/09/11 13:17:10 lord
+ * Added identifiable support
+ *
+ * Revision 1.3 2000/06/27 16:11:46 lord
+ * Added event handling to the "clear" method which clearly needs it
+ *
+ * Revision 1.2 2000/06/13 11:02:58 lord
+ * Fixed event handling
+ *
+ * Revision 1.1 2000/06/05 14:46:25 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/group/SequenceGroup.java b/src/uk/ac/man/bioinf/sequence/group/SequenceGroup.java
new file mode 100644
index 0000000..471318a
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/group/SequenceGroup.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.group; // Package name inserted by JPack
+
+import java.util.Iterator;
+import uk.ac.man.bioinf.sequence.Sequence;
+
+/**
+ * SequenceGroup.java
+ *
+ * This interface defines a SequenceGroup that is capable of storing a
+ * collection of sequences. It would usually be expected that the
+ * sequences in the group would usually have something in common with
+ * each other, being for instance some of the members of a
+ * SequenceAlignment, although this is not required.
+ *
+ * Created: Thu Jun 1 18:09:32 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceGroup.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceGroup
+{
+ /**
+ * Adds a sequence to this group
+ * @param seq the sequence
+ */
+ public void addSequenceToGroup( Sequence seq );
+
+ /**
+ * Removes a sequence from this group
+ * @param seq the sequence
+ */
+ public void removeSequenceFromGroup( Sequence seq );
+
+ /**
+ * Does this group contain the sequence
+ * @param seq the sequence
+ * @return true if containined
+ */
+ public boolean containsSequence( Sequence seq );
+
+ /**
+ * Get all the sequences in this group.
+ * @return
+ */
+ public Sequence[] getSequences();
+
+ /**
+ * Empty the group of sequences
+ */
+ public void clearSequences();
+
+ /**
+ * Return the number of sequences in this group.
+ * @return the number
+ */
+ public int getNumberSequences();
+
+ /**
+ * Returns an iterator of all the sequences. This should be fail
+ * fast if the group is modified whilst the iterator is being used.
+ * @return
+ */
+ public Iterator iterator();
+
+}// SequenceGroup
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceGroup.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/10/26 12:42:49 jns
+ * o added editing facilities to SA - this includes insertion/deletion of gaps,
+ * addition/removal of sequences from an alignment. It involved resolving some
+ * conflicts with the group stuff.
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/06/05 14:46:26 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.java b/src/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.java
new file mode 100644
index 0000000..baa7992
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/AbstractIdentifier.java
@@ -0,0 +1,80 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * AbstractSequenceIdentifier.java
+ *
+ *
+ * Created: Wed Jul 5 16:00:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractIdentifier.java,v 1.3 2001/05/24 15:36:13 lord Exp $
+ */
+
+public abstract class AbstractIdentifier implements Identifier
+{
+ private Source source;
+
+ public AbstractIdentifier( Source source )
+ {
+ this.source = source;
+ }
+
+ public Source getSource()
+ {
+ return source;
+ }
+
+ public void setSource( Source source )
+ {
+ this.source = source;
+ }
+} // AbstractSequenceIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractIdentifier.java,v $
+ * Revision 1.3 2001/05/24 15:36:13 lord
+ * The source is not mutable.
+ *
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.java b/src/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.java
new file mode 100644
index 0000000..4cc4292
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/DatabaseIdentifier.java
@@ -0,0 +1,82 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * DatabaseIdentifier.java
+ *
+ *
+ * Created: Wed Jul 5 14:11:46 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DatabaseIdentifier.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class DatabaseIdentifier extends AbstractIdentifier
+{
+
+ private String accession, databaseName;
+
+ public DatabaseIdentifier( Source source, String accession )
+ {
+ super( source );
+ this.accession = accession;
+ }
+
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ public abstract String getDatabaseName();
+
+ public String getTitle()
+ {
+ return accession;
+ }
+
+} // DatabaseIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: DatabaseIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/FileSource.java b/src/uk/ac/man/bioinf/sequence/identifier/FileSource.java
new file mode 100644
index 0000000..0f2c5d5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/FileSource.java
@@ -0,0 +1,75 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+import java.io.File;
+
+
+/**
+ * FileSource.java
+ *
+ *
+ * Created: Fri Sep 8 18:57:27 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: FileSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class FileSource implements Source
+{
+ private File file;
+
+ public FileSource( File file )
+ {
+ this.file = file;
+ }
+
+ public File getFile()
+ {
+ return file;
+ }
+
+ public String getTitle()
+ {
+ return file.getName();
+ }
+} // FileSource
+
+
+
+/*
+ * ChangeLog
+ * $Log: FileSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/Identifiable.java b/src/uk/ac/man/bioinf/sequence/identifier/Identifiable.java
new file mode 100644
index 0000000..255ff59
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/Identifiable.java
@@ -0,0 +1,63 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * Identifiable.java
+ *
+ *
+ * Created: Wed Jul 5 16:04:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Identifiable.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Identifiable
+{
+ public Identifier getIdentifier();
+
+} // Identifiable
+
+
+
+/*
+ * ChangeLog
+ * $Log: Identifiable.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/Identifier.java b/src/uk/ac/man/bioinf/sequence/identifier/Identifier.java
new file mode 100644
index 0000000..e90e976
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/Identifier.java
@@ -0,0 +1,81 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * SequenceIdentifier.java
+ *
+ *
+ * Created: Mon Jul 3 16:07:39 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Identifier.java,v 1.3 2001/05/24 15:36:13 lord Exp $
+ */
+
+public interface Identifier
+{
+ /**
+ * This returns the source of the sequence. This might be a File
+ * object if the sequence has been read straight from file, or a URL
+ * from the internet. Alternatively it could be a Java Obect
+ * reference if the sequence has been retrieved by calculation, say
+ * of a Consensus.
+ * @return
+ */
+ public Source getSource();
+
+ public void setSource( Source source );
+ /**
+ * Gets a human readable title for the Sequence
+ * @return
+ */
+ public String getTitle();
+} // SequenceIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: Identifier.java,v $
+ * Revision 1.3 2001/05/24 15:36:13 lord
+ * The source is not mutable.
+ *
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.java b/src/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.java
new file mode 100644
index 0000000..7a8646e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/MalformedAccessionException.java
@@ -0,0 +1,64 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * MalformedAccessionException.java
+ *
+ * Used to indicate an inappropriate accession number has been
+ * entered.
+ *
+ * Created: Wed Jul 5 14:17:19 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: MalformedAccessionException.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class MalformedAccessionException extends IllegalArgumentException
+{
+
+ public MalformedAccessionException( String message )
+ {
+ super( message );
+ }
+} // MalformedAccessionException
+
+
+
+/*
+ * ChangeLog
+ * $Log: MalformedAccessionException.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.java b/src/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.java
new file mode 100644
index 0000000..c6cc31d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/NoIdentifier.java
@@ -0,0 +1,92 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * NoSequenceIdentifier.java
+ *
+ *
+ * Created: Wed Jul 5 18:42:11 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NoIdentifier.java,v 1.3 2001/05/24 15:36:13 lord Exp $
+ */
+
+public class NoIdentifier implements Identifier
+{
+
+ private final static Source noSource = new NoSource();
+ private final static String noTitle = "No Title";
+ private Source source = noSource;
+
+ public NoIdentifier()
+ {
+ }
+
+ public NoIdentifier( Source source )
+ {
+ this.source = source;
+ }
+
+ public Source getSource()
+ {
+ return source;
+ }
+
+ public void setSource( Source source )
+ {
+ this.source = source;
+ }
+
+ public String getTitle()
+ {
+ return noTitle;
+ }
+} // NoSequenceIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoIdentifier.java,v $
+ * Revision 1.3 2001/05/24 15:36:13 lord
+ * The source is not mutable.
+ *
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/NoSource.java b/src/uk/ac/man/bioinf/sequence/identifier/NoSource.java
new file mode 100644
index 0000000..b669fb6
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/NoSource.java
@@ -0,0 +1,67 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * NoSource.java
+ *
+ *
+ * Created: Wed Jul 5 18:11:08 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: NoSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class NoSource implements Source
+{
+
+ private static final String noTitle = "No Title";
+ public String getTitle()
+ {
+ return noTitle;
+ }
+} // NoSource
+
+
+
+/*
+ * ChangeLog
+ * $Log: NoSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/ReaderSource.java b/src/uk/ac/man/bioinf/sequence/identifier/ReaderSource.java
new file mode 100644
index 0000000..83ec0cb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/ReaderSource.java
@@ -0,0 +1,69 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+import java.io.Reader;
+
+
+/**
+ * ReaderSource.java
+ *
+ * This class identify the specific reader which was used to load the
+ * identifiable object. There is not really a lot which can be done
+ * with an object cast as a Reader, so essentially it just uses its
+ * toString method at the time that its called.
+ *
+ * Created: Fri Sep 8 18:15:25 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ReaderSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ReaderSource extends SimpleSource
+{
+
+ public ReaderSource( Reader reader )
+ {
+ super( reader.toString() );
+ }
+
+} // ReaderSource
+
+
+
+/*
+ * ChangeLog
+ * $Log: ReaderSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/SequenceSource.java b/src/uk/ac/man/bioinf/sequence/identifier/SequenceSource.java
new file mode 100644
index 0000000..33fdc94
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/SequenceSource.java
@@ -0,0 +1,68 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * SequenceSource.java
+ *
+ * This class represents the source that is used to produce a
+ * sequence. Source means for example, the physical location, or means
+ * that were used to retrieve this sequence, such as file name, URL,
+ * or the name of the program that was used to retrieve the sequence.
+ *
+ * Created: Tue Jul 4 14:50:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface SequenceSource
+{
+ /**
+ * Get the human readable name for this SequenceSource
+ * @return
+ */
+ public String getTitle();
+
+} // SequenceSource
+
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.java b/src/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.java
new file mode 100644
index 0000000..26cf4a5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/SimpleIdentifier.java
@@ -0,0 +1,81 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * SimpleIdentifier.java
+ *
+ *
+ * Created: Wed Jul 5 19:30:33 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SimpleIdentifier.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SimpleIdentifier extends AbstractIdentifier
+{
+ private String title;
+
+ public SimpleIdentifier( String title )
+ {
+ this( title, new NoSource() );
+ }
+
+ public SimpleIdentifier( String title, Source source )
+ {
+ super( source );
+ this.title = title;
+ }
+
+ public String getTitle()
+ {
+ return title;
+ }
+} // SimpleIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: SimpleIdentifier.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/10/31 15:50:56 lord
+ * Added new constructor
+ *
+ * Revision 1.2 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/SimpleSource.java b/src/uk/ac/man/bioinf/sequence/identifier/SimpleSource.java
new file mode 100644
index 0000000..5b759aa
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/SimpleSource.java
@@ -0,0 +1,70 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * SimpleSource.java
+ *
+ * Utility class mainly meant to extend from.
+ *
+ * Created: Fri Sep 8 18:18:15 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SimpleSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SimpleSource implements Source
+{
+ private String title;
+
+ public SimpleSource( String title )
+ {
+ this.title = title;
+ }
+
+ public String getTitle()
+ {
+ return title;
+ }
+} // SimpleSource
+
+
+
+/*
+ * ChangeLog
+ * $Log: SimpleSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/Source.java b/src/uk/ac/man/bioinf/sequence/identifier/Source.java
new file mode 100644
index 0000000..c510ccf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/Source.java
@@ -0,0 +1,73 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * SequenceSource.java
+ *
+ * This class represents the source that is used to produce a
+ * sequence. Source means for example, the physical location, or means
+ * that were used to retrieve this sequence, such as file name, URL,
+ * or the name of the program that was used to retrieve the sequence.
+ *
+ * Created: Tue Jul 4 14:50:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Source.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Source
+{
+ /**
+ * Get the human readable name for this SequenceSource
+ * @return
+ */
+ public String getTitle();
+
+} // SequenceSource
+
+
+
+
+/*
+ * ChangeLog
+ * $Log: Source.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.java b/src/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.java
new file mode 100644
index 0000000..ce83ef2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/StreamSequenceSource.java
@@ -0,0 +1,76 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+import java.io.Reader;
+
+
+/**
+ * StreamSequenceSource.java
+ *
+ *
+ * Created: Tue Jul 4 17:30:29 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: StreamSequenceSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class StreamSequenceSource implements SequenceSource
+{
+ private Reader reader;
+ private String format;
+
+ public StreamSequenceSource( Reader reader, String format )
+ {
+ this.reader = reader;
+ this.format = format;
+ }
+
+ public String getFormat()
+ {
+ return format;
+ }
+
+ public Reader getReader()
+ {
+ return reader;
+ }
+} // StreamSequenceSource
+
+
+
+/*
+ * ChangeLog
+ * $Log: StreamSequenceSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.java b/src/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.java
new file mode 100644
index 0000000..68647f2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/SwissProtIdentifier.java
@@ -0,0 +1,81 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+
+
+/**
+ * SwissProtIdentifier.java
+ *
+ *
+ * Created: Wed Jul 5 14:16:55 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SwissProtIdentifier.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SwissProtIdentifier extends DatabaseIdentifier
+{
+
+ public SwissProtIdentifier( Source source, String accessionNumber ) throws MalformedAccessionException
+ {
+ super( source, accessionNumber );
+ if( isAccesionMad( accessionNumber ) ){
+ throw new MalformedAccessionException( "This is not a valid Swiss-prot accession number" );
+ }
+ }
+
+ private boolean isAccesionMad( String accession )
+ {
+ // (PENDING:- PL) Actually need to write this!!!
+ return false;
+ }
+
+ public String getDatabaseName()
+ {
+ return "swiss-prot";
+ }
+
+} // SwissProtIdentifier
+
+
+
+/*
+ * ChangeLog
+ * $Log: SwissProtIdentifier.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/09/11 13:06:43 lord
+ * Changed name of SequenceIdentifier, and SequenceSource to
+ * Identifier and Source, which makes these a little bit more generic
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.java b/src/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.java
new file mode 100644
index 0000000..3c4913f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/identifier/URLSequenceSource.java
@@ -0,0 +1,78 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.identifier; // Package name inserted by JPack
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.URL;
+
+
+/**
+ * URLSequenceSource.java
+ *
+ * A source for a sequence stored at a URL.
+ *
+ * Created: Tue Jul 4 17:47:31 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: URLSequenceSource.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class URLSequenceSource extends StreamSequenceSource
+{
+ private URL url;
+
+ public URLSequenceSource( URL url, String format) throws IOException
+ {
+ super( new InputStreamReader( url.openStream() ), format );
+ this.url = url;
+ }
+
+ public URL getURL()
+ {
+ return url;
+ }
+
+ public String getTitle()
+ {
+ return "URL:- "+ url.toString();
+ }
+} // URLSequenceSource
+
+
+
+/*
+ * ChangeLog
+ * $Log: URLSequenceSource.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/18 12:38:31 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/package.html b/src/uk/ac/man/bioinf/sequence/package.html
new file mode 100644
index 0000000..fa521a4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/package.html
@@ -0,0 +1,12 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html>
+ <head>
+ <title>uk.ac.man.bioinf.sequence</title>
+ </head>
+
+ <body>
+ Provides classes for representing mutable sequences.
+ As well as providing interfaces which represent the notion of a
+ sequence, a full event model is provided.
+ </body>
+</html>
\ No newline at end of file
diff --git a/src/uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.java b/src/uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.java
new file mode 100644
index 0000000..2e62fe1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/ComplexElementAndModificationTest.java
@@ -0,0 +1,256 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.complex.ComplexElement;
+import uk.ac.man.bioinf.sequence.complex.Methylation;
+import uk.ac.man.bioinf.sequence.complex.ModificationFactory;
+import uk.ac.man.bioinf.sequence.complex.ComplexElementFactory;
+import uk.ac.man.bioinf.sequence.complex.Modification;
+import uk.ac.man.bioinf.sequence.types.RNANucleotide;
+
+
+/**
+ * ComplexElementAndModificationTest.java
+ *
+ *
+ * Created: Tue Feb 29 11:32:15 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexElementAndModificationTest.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ComplexElementAndModificationTest
+{
+
+ public static void main( String[] args )
+ {
+ System.out.println( "This class tests out the ComplexElement, and associated Factory methods" );
+ System.out.println( "The essential rules are as follows:- " );
+ System.out.println();
+
+ System.out.println( "1) A request for a given modification to an specific Residue should always return" );
+ System.out.println( "the same object" );
+ System.out.println();
+
+ System.out.println( "2) A complex element with a given set of modifications to a given residue should " );
+ System.out.println( "always return the same object no matter what order the modifications are obtained" );
+ System.out.println();
+
+ System.out.println( "3) Modifications will be addressed in two ways. Either by name or by subclassing as singletons" );
+ System.out.println( "or enumerations (the latter is not supported yet!). All modifications instances should have" );
+ System.out.println( "different names however they are created. The factory should crash if duplicates are used" );
+ System.out.println();
+
+ System.out.println( "4) Although not tested by this class, performance should be good. The initial implementation has" );
+ System.out.println( "performs look up in something approximately constant time, wrt to the number of ComplexElements in" );
+ System.out.println( "existance, and linear wrt to the number of modifications to the ComplexElement in question" );
+ System.out.println( "**************" );
+ System.out.println();
+
+ System.out.println( "Testing Modifications to residues" );
+ System.out.println( "Using the " + RNANucleotide.ADENOSINE );
+ System.out.println();
+
+ System.out.println( "Attempting to gain the methylated version " );
+
+ ComplexElement methylA = ComplexElementFactory.addComplexElement( RNANucleotide.ADENOSINE, Methylation.METHYLATION );
+
+ System.out.println( "Have instance " + methylA );
+ System.out.println();
+
+ System.out.println( "Retrieving for a second time..." );
+
+ ComplexElement methylASecond = ComplexElementFactory.addComplexElement( RNANucleotide.ADENOSINE, Methylation.METHYLATION );
+ System.out.println( "Have second instance " + methylASecond );
+ System.out.println();
+
+ System.out.println( "Testing that these objects have same hash, and .equals, and == " );
+ System.out.println( "Hash codes are " + methylA.hashCode() + " and " + methylASecond.hashCode() );
+ System.out.println( "First is equal to the second " + methylA.equals( methylASecond ) );
+ System.out.println( "First is == to the second " + (methylA == methylASecond ) );
+ System.out.println( "************" );
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Testing out modification factory with generic \"phospho\" element" );
+
+ System.out.println( "Initial retrieval....should throw exception as this element has not been created" );
+
+ Modification phospho = null;
+
+ try{
+ phospho = getPhosphoModification();
+ System.out.println( "ERROR: The attempt to gain a modification should have failed " );
+ Thread.dumpStack();
+ System.exit( 1 );
+ }
+ catch( Exception exp ){
+ System.out.println( "Have caught the exception correctly \n " + exp.getMessage() );
+ }
+ System.out.println();
+
+ System.out.println( "Attempting to create the phospho element " );
+ try{
+ phospho = createPhospoModification();
+ System.out.println( "Modification created correctly " );
+ }
+ catch( Exception exp ){
+ System.out.println( "ERROR: First attempt to create a modification has failed" );
+ }
+ System.out.println();
+
+ System.out.println( "Attempting to re-create the phospho element. Should except" );
+ try{
+ phospho = createPhospoModification();
+ System.out.println( "ERROR: Attempt to re-create the phospo element should have failed " );
+ }
+ catch( Exception exp ){
+ System.out.println( "Have caught the exception correctly \n " + exp.getMessage() );
+ }
+ System.out.println();
+
+ System.out.println( "Also checking to see whether we get an exception when attempting to " );
+ System.out.println( "create the methylation modification again" );
+
+ try{
+ ModificationFactory.createModification( "Methylation", '*' );
+ System.out.println( "ERROR: Attempt to re-create the methyl element should have failed " );
+ }
+ catch( Exception exp ){
+ System.out.println( "Have caught the exception correctly \n " + exp.getMessage() );
+ }
+ System.out.println( "Exception testing complete" );
+ System.out.println( "*************" );
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Testing whether multiple retrieval of phospho are equal " );
+ Modification phospho2 = getPhosphoModification();
+
+ System.out.println( "Hash codes are " + phospho.hashCode() + " " + phospho2.hashCode() );
+ System.out.println( "First is equal to the second " + phospho.equals( phospho2 ) );
+ System.out.println( "First is == to the second " + ( phospho == phospho2 ) );
+
+ System.out.println( "Multiple Modifications retrieval testing complete" );
+ System.out.println( "*************" );
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Testing associativity of the ComplexElement Retrieval" );
+ System.out.println( "Retrieveing phosopho A element " );
+ ComplexElement phosphoA = ComplexElementFactory.addComplexElement( RNANucleotide.ADENOSINE, phospho );
+ System.out.println( "Have phospho A " + phosphoA );
+
+ System.out.println( "Modifications to phosphoA :- " );
+ printModifications( phosphoA.getModifications() );
+ System.out.println( "Modifications to methylA :- " );
+ printModifications( methylA.getModifications() );
+
+ System.out.println( "Now getting phosphoMethylA, and MethylPhosphoA " );
+ ComplexElement phosphoMethylA = ComplexElementFactory.addComplexElement( phosphoA, Methylation.METHYLATION );
+ ComplexElement methylPhosphoA = ComplexElementFactory.addComplexElement( methylA, phospho );
+
+ Modification[] phosMethMod = phosphoMethylA.getModifications();
+ Modification[] methPhosMod = methylPhosphoA.getModifications();
+
+ System.out.println( "Modifications to phosphoMethylA are :- " );
+ printModifications( phosMethMod );
+ System.out.println( "Modifications to methylPhosphoA are :- " );
+ printModifications( methPhosMod );
+ System.out.println();
+
+ System.out.println( "Hash codes are " + methylPhosphoA.hashCode() + " " + phosphoMethylA.hashCode() );
+ System.out.println( "First is equal to the second " + methylPhosphoA.equals( phosphoMethylA ) );
+ System.out.println( "First is == to the second " + ( methylPhosphoA == phosphoMethylA ) );
+ System.out.println( "Associative testing complete" );
+ System.out.println( "**********************" );
+
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Testing out removal" );
+ ComplexElement phosMethModAMinusPhos = ComplexElementFactory.removeComplexElement
+ ( phosphoMethylA, Methylation.METHYLATION );
+ System.out.println( "Have remove methyl from A " );
+ System.out.println( "Element should equal phosphoA " );
+ System.out.println( "which is " + phosMethModAMinusPhos.equals( phosphoA ) );
+ System.out.println( "and == " + ( phosMethModAMinusPhos == phosphoA ) );
+
+
+ System.out.println( "Finished test!" );
+
+ }
+
+ private static void printModifications( Modification mod )
+ {
+ System.out.println( " " + mod + mod.getName() );
+ }
+
+ private static void printModifications( Modification[] mods )
+ {
+ for( int i = 0 ; i < mods.length ; i ++ ){
+ System.out.println( " " + mods[ i ] + mods[ i ].getName() );
+ } //end for( i < mods.length )
+ }
+
+ private static Modification createPhospoModification()
+ {
+ return ModificationFactory.createModification( "Phospho", 'p' );
+ }
+
+ private static Modification getPhosphoModification()
+ {
+ return ModificationFactory.getModification( "Phospho" );
+ } //end main method
+
+
+} // ComplexElementAndModificationTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexElementAndModificationTest.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/11/27 18:14:58 lord
+ * *** empty log message ***
+ *
+ * Revision 1.2 2000/04/18 17:52:27 jns
+ * o changes madde because of files moved to types package.
+ *
+ * Revision 1.1 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.java b/src/uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.java
new file mode 100644
index 0000000..ae8a487
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/ComplexSequenceTest.java
@@ -0,0 +1,187 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.InvalidSequenceTypeException;
+import uk.ac.man.bioinf.sequence.Residue;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.complex.ComplexSequence;
+import uk.ac.man.bioinf.sequence.complex.DefaultComplexSequence;
+import uk.ac.man.bioinf.sequence.complex.DefaultComplexSequenceType;
+import uk.ac.man.bioinf.sequence.complex.Methylation;
+import uk.ac.man.bioinf.sequence.complex.Modification;
+import uk.ac.man.bioinf.sequence.complex.ModificationFactory;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.types.RNANucleotide;
+import uk.ac.man.bioinf.sequence.types.RNASequenceType;
+
+
+/**
+ * ComplexSequenceTest.java
+ *
+ *
+ * Created: Mon Nov 27 14:09:29 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ComplexSequenceTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ComplexSequenceTest
+{
+ public static void main( String[] args ) throws Throwable
+ {
+ System.out.println( "First testing construction of the an RNA sequence " );
+ Modification[] mods =
+ {
+ Methylation.METHYLATION
+ };
+
+ ComplexSequence seq = new DefaultComplexSequence( createRNAResidues(), new DefaultComplexSequenceType
+ ( RNASequenceType.getInstance(),
+ mods,
+ "Methylated RNA "),
+ new NoIdentifier() );
+
+ System.out.println( "Have sequence of " + seq.getLength() + " length" );
+ Sequences.printSequence( seq );
+
+
+ System.out.println( "Now trying to methylate some residues" );
+
+ seq.addModificationAt( Methylation.METHYLATION, 4);
+ seq.addModificationAt( Methylation.METHYLATION, 5);
+ seq.addModificationAt( Methylation.METHYLATION, 8);
+
+ Sequences.printSequence( seq );
+
+ System.out.println( "Now attempting to phosphorylate an element (should fail ) " );
+ Modification phospho = ModificationFactory.createModification( "Phospho", 'p' );
+
+ try{
+ seq.addModificationAt( phospho, 6 );
+ }
+ catch( InvalidSequenceTypeException exp ) {
+ System.out.println( "Exception caught correctly " );
+ }
+
+ System.out.println( "Starting again with phospho included in type" );
+ Modification[] mods2 =
+ {
+ Methylation.METHYLATION,
+ phospho
+ };
+
+
+ seq = new DefaultComplexSequence( createRNAResidues(), new DefaultComplexSequenceType
+ ( RNASequenceType.getInstance(),
+ mods2,
+ "Methylated RNA "),
+ new NoIdentifier() );
+
+
+ Sequences.printSequence( seq );
+
+ seq.addModificationAt( Methylation.METHYLATION, 4);
+ seq.addModificationAt( Methylation.METHYLATION, 5);
+ seq.addModificationAt( Methylation.METHYLATION, 8);
+
+ Sequences.printSequence( seq );
+
+ seq.addModificationAt( phospho, 4);
+ seq.addModificationAt( phospho, 10);
+ seq.addModificationAt( phospho, 8);
+
+ Sequences.printSequence( seq );
+
+
+ } //end main method
+
+ public static Residue[] createRNAResidues()
+ {
+ Residue[] res =
+ {
+
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.ADENOSINE,
+ RNANucleotide.URACIL,
+ RNANucleotide.CYTOSINE,
+ RNANucleotide.GUANINE,
+ RNANucleotide.URACIL
+ };
+ return res;
+ }
+} // ComplexSequenceTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: ComplexSequenceTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/27 18:14:59 lord
+ * *** empty log message ***
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/test/EditableSequenceTest.java b/src/uk/ac/man/bioinf/sequence/test/EditableSequenceTest.java
new file mode 100644
index 0000000..c866106
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/EditableSequenceTest.java
@@ -0,0 +1,241 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import java.util.Random;
+import uk.ac.man.bioinf.sequence.DefaultEditableSequence;
+import uk.ac.man.bioinf.sequence.EditableSequence;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.identifier.NoIdentifier;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * EditableSequenceTest.java
+ *
+ *
+ * Created: Fri Mar 3 16:08:35 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: EditableSequenceTest.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class EditableSequenceTest
+{
+ public static void main( String[] args )
+ {
+ System.out.println( "This class tests out the DefaultEditableSequenceClass. Its is designed to test " );
+ System.out.println( "that the class allows correct editing of sequences and further signals the correct " );
+ System.out.println( "events" );
+
+ System.out.println( "First make a series of elements up to test the sequence out " );
+
+ AminoAcid[] elems = AminoAcid.getAll();
+
+ DefaultEditableSequence seq = new DefaultEditableSequence( elems, ProteinSequenceType.getInstance(),
+ new NoIdentifier() );
+
+ printSeq( seq );
+ System.out.println( "*************" );
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Testing out alteration, addition and removal of elements " );
+ alterSeq( seq );
+ System.out.println( "Editability testing complete" );
+ System.out.println( "****************************" );
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Testing out listening abilities" );
+ System.out.println( "Adding sequence listener to sequence " );
+ SequenceListener seqList = new SequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ System.out.println( event );
+ }
+ };
+
+ seq.addSequenceListener( seqList );
+
+ System.out.println( "Repeating addn removal tests. The listner should print out the event for each of the change events" );
+ alterSeq( seq );
+ System.out.println( "Removing listener " );
+ seq.removeSequenceListener( seqList );
+ System.out.println( "Listener tests complete" );
+ System.out.println( "***********************" );
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Now testing with a compliant veto listener" );
+ VetoableSequenceListener compList = new VetoableSequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ System.out.println( event );
+ }
+ public void vetoableChangeOccurred( VetoableSequenceEvent event )
+ {
+ System.out.println( event );
+ }
+ };
+ seq.addVetoableSequenceListener( compList );
+ alterSeq( seq );
+ seq.removeSequenceListener( compList );
+
+ System.out.println( "Compliant listener tests complete" );
+ System.out.println( "*********************************" );
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Testing with a non compliant listener" );
+ System.out.println( "These should give rise to exceptions which are caught" );
+ VetoableSequenceListener nonComp = new VetoableSequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ System.out.println( event );
+ }
+
+ public void vetoableChangeOccurred( VetoableSequenceEvent event ) throws SequenceVetoException
+ {
+ System.out.println( event );
+ System.out.println( "Now throwing veto to this event " );
+ throw new SequenceVetoException( "Blarrrgh", event );
+ }
+ };
+ seq.addVetoableSequenceListener( nonComp );
+ alterSeq( seq );
+ System.out.println( "Non Compliant Listener test complete" );
+ System.out.println( "************************************" );
+
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Test class complete" );
+ } //end main method
+
+ public static void printSeq( Sequence seq )
+ {
+ System.out.println( "The elements making up this sequence are :- " );
+ System.out.println( String.valueOf( seq.getSequenceAsChars() ) );
+ }
+
+ private static void alterSeq( EditableSequence seq )
+ {
+ alterElement( seq );
+ insertAndRemoveElement( seq );
+ }
+
+
+ private static void alterElement( EditableSequence seq )
+ {
+ try{
+ Random rand = new Random();
+
+ int index = rand.nextInt( seq.getLength() - 1 ) + 1;
+
+ System.out.println( "Changing the element at " + index + " to glycine" );
+ Element old = seq.setElementAt( AminoAcid.GLYCINE, index );
+
+ System.out.println( "Sequence is now " );
+ printSeq( seq );
+
+ System.out.println( "Changing sequence back " );
+ seq.setElementAt( old, index );
+ printSeq( seq );
+ }
+ catch( SequenceVetoException sve ){
+ System.out.println( "There has been a veto" );
+ System.out.println( sve );
+ }
+ }
+
+ private static void insertAndRemoveElement( EditableSequence seq )
+ {
+ try{
+ Random rand = new Random();
+
+ int index = rand.nextInt( seq.getLength() - 1 ) + 1;
+
+ System.out.println( "Inserting a glycine at " + index );
+ seq.insertElementAt( AminoAcid.GLYCINE, index );
+
+ System.out.println( "Sequence is now:- " );
+ printSeq( seq );
+
+ System.out.println( "Now removing this element " );
+
+ System.out.println( "Removal: " + seq.deleteElementAt( index ) );
+ }
+ catch( SequenceVetoException sve ){
+ }
+ }
+} // EditableSequenceTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: EditableSequenceTest.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/09/15 17:04:57 lord
+ * Updated due to change in SequenceIdentifier name
+ *
+ * Revision 1.3 2000/07/18 12:38:54 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.2 2000/04/18 17:52:27 jns
+ * o changes madde because of files moved to types package.
+ *
+ * Revision 1.1 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ */
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/test/GappableSequenceTest.java b/src/uk/ac/man/bioinf/sequence/test/GappableSequenceTest.java
new file mode 100644
index 0000000..07fcbf0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/GappableSequenceTest.java
@@ -0,0 +1,215 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import java.util.Random;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * GappableSequenceTest.java
+ *
+ *
+ * Created: Tue Mar 7 13:45:10 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GappableSequenceTest.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class GappableSequenceTest
+{
+ public static void main( String[] args )
+ {
+ System.out.println( "This class tests out the DefaultGappedSequenceClass. Its is designed to test " );
+ System.out.println( "that the class allows correct editing of sequences and further signals the correct " );
+ System.out.println( "events" );
+
+ System.out.println( "First make a series of elements up to test the sequence out " );
+
+ Thread.dumpStack();
+
+ AminoAcid[] elems = AminoAcid.getAll();
+
+ DefaultGappedSequence seq = new DefaultGappedSequence( elems, ProteinSequenceType.getInstance() );
+
+ System.out.println( "The value of the element at 20 is" + seq.getGappedElementAt( 20 ).toChar());
+
+ printSeq( seq );
+ System.out.println( "*************" );
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Testing out alteration, addition and removal of elements " );
+ alterSeq( seq );
+
+ System.out.println( "Editability testing complete" );
+ System.out.println( "****************************" );
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Testing out listening abilities" );
+ System.out.println( "Adding sequence listener to sequence " );
+ SequenceListener seqList = new SequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ System.out.println( event );
+ }
+ };
+
+ seq.addSequenceListener( seqList );
+
+ System.out.println( "Repeating addn removal tests. The listner should print out the event for each of the change events" );
+ alterSeq( seq );
+ System.out.println( "Removing listener " );
+ seq.removeSequenceListener( seqList );
+ System.out.println( "Listener tests complete" );
+ System.out.println( "***********************" );
+ System.out.println();
+ System.out.println();
+
+
+ System.out.println( "Now testing with a compliant veto listener" );
+ VetoableSequenceListener compList = new VetoableSequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ System.out.println( event );
+ }
+ public void vetoableChangeOccurred( VetoableSequenceEvent event )
+ {
+ System.out.println( event );
+ }
+ };
+ seq.addVetoableSequenceListener( compList );
+ alterSeq( seq );
+ seq.removeSequenceListener( compList );
+
+ System.out.println( "Compliant listener tests complete" );
+ System.out.println( "*********************************" );
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Testing with a non compliant listener" );
+ System.out.println( "These should give rise to exceptions which are caught" );
+ VetoableSequenceListener nonComp = new VetoableSequenceListener(){
+ public void changeOccurred( SequenceEvent event )
+ {
+ System.out.println( event );
+ }
+
+ public void vetoableChangeOccurred( VetoableSequenceEvent event ) throws SequenceVetoException
+ {
+ System.out.println( event );
+ System.out.println( "Now throwing veto to this event " );
+ throw new SequenceVetoException( "Blarrrgh", event );
+ }
+ };
+ seq.addVetoableSequenceListener( nonComp );
+ alterSeq( seq );
+ System.out.println( "Non Compliant Listener test complete" );
+ System.out.println( "************************************" );
+
+ System.out.println();
+ System.out.println();
+
+ System.out.println( "Test class complete" );
+ } //end main method
+
+ public static void printSeq( GappedSequence seq )
+ {
+ System.out.println( "The elements making up this sequence are :- " );
+ System.out.println( String.valueOf( seq.getSequenceAsChars() ) );
+ System.out.println( "The gapped elements making up this sequence are :- " );
+ System.out.println( String.valueOf( seq.getGappedSequenceAsChars() ) );
+ }
+
+ private static void alterSeq( GappedSequence seq )
+ {
+ insertAndRemoveElement( seq );
+ }
+
+ private static void insertAndRemoveElement( GappedSequence seq )
+ {
+ try{
+ Random rand = new Random();
+
+ int index = rand.nextInt( seq.getLength() - 1 ) + 1;
+
+ System.out.println( "Inserting a gap at " + index );
+ seq.insertGapAt( index );
+
+ System.out.println( "Sequence is now:- " );
+ printSeq( seq );
+
+ System.out.println( "Now removing this gap" );
+
+ seq.deleteGapAt( index );
+
+ System.out.println( "After removal" );
+ printSeq( seq );
+
+ }
+ catch( SequenceVetoException sve ){
+ }
+ }
+} // GappedSequenceTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: GappableSequenceTest.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2000/07/18 12:38:54 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.4 2000/06/13 11:02:29 lord
+ * Boring changes
+ *
+ * Revision 1.3 2000/04/18 17:52:27 jns
+ * o changes madde because of files moved to types package.
+ *
+ * Revision 1.2 2000/03/16 16:20:34 lord
+ * Boring changes
+ *
+ * Revision 1.1 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/test/GappedSequenceTest.java b/src/uk/ac/man/bioinf/sequence/test/GappedSequenceTest.java
new file mode 100644
index 0000000..a551835
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/GappedSequenceTest.java
@@ -0,0 +1,134 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import java.util.Random;
+import uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch;
+import uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.GappedSequence;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+
+
+/**
+ * GappedSequenceTest.java
+ *
+ *
+ * Created: Wed Jun 7 16:18:11 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: GappedSequenceTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class GappedSequenceTest
+{
+
+ public static void main( String[] args ) throws Throwable
+ {
+ System.out.println( "This is a test to make sure that the DefaultGappedSequence class is working" );
+ System.out.println( "Events are not tested in this class" );
+
+ GappedSequence seq;
+
+ if( false ){
+ AminoAcid[] elems = AminoAcid.getAll();
+
+ seq = new DefaultGappedSequence( elems, ProteinSequenceType.getInstance() );
+ }
+ else{
+ seq = CinemaTestLaunch.generateMsa().getSequenceAt( 2 );
+ }
+
+ reportLength( seq );
+
+ System.out.println( "Inserting several random gaps" );
+
+ for( int i = 0; i < 10; i++ ){
+ Random rand = new Random();
+
+ int index = rand.nextInt( seq.getLength() - 1 ) + 1;
+
+ System.out.println( "Inserting a gap at " + index );
+ seq.insertGapAt( index );
+ }
+
+ reportLength( seq );
+
+ try{
+ System.out.println( "Attempting to get element before start " );
+ seq.getElementAt( 0 );
+ }
+ catch( Exception exp ){
+ System.out.println( "Caught " + exp );
+ }
+
+ try{
+ System.out.println( "Attempting to get element after end " );
+ seq.getElementAt( 30 );
+ }
+ catch( Exception exp ){
+ System.out.println( "Caught " + exp );
+ }
+
+ try{
+ System.out.println( "Attempt to get gapped element before start " );
+ seq.getGappedElementAt( 0 );
+ }
+ catch( Exception exp ){
+ System.out.println( "Caught " + exp );
+ }
+
+ try{
+ System.out.println( "Attempt to get gapped elemnt after end " );
+ seq.getGappedElementAt( 590 );
+ }
+ catch( Exception exp ){
+ System.out.println( "Caught " + exp );
+ }
+ } //end main method
+
+ private static void reportLength( GappedSequence seq )
+ {
+ System.out.println( "Sequence is " + seq.getLength() + " whilst gapped length is " + seq.getGappedLength() );
+ }
+
+} // GappedSequenceTest
+
+
+
+
+/*
+ * ChangeLog
+ * $Log: GappedSequenceTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/06/13 11:02:29 lord
+ * Boring changes
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.java b/src/uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.java
new file mode 100644
index 0000000..2da362f
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/SequenceAlignmentTest.java
@@ -0,0 +1,246 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.DefaultGappedSequence;
+import uk.ac.man.bioinf.sequence.alignment.DefaultSequenceAlignment;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceListener;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.VetoableSequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceVetoException;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.VetoableAlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentVetoException;
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+
+
+/**
+ * SequenceAlignmentTest.java
+ *
+ *
+ * Created: Fri Mar 10 12:39:40 2000
+ *
+ * @author J Selley
+ * @version $Id: SequenceAlignmentTest.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceAlignmentTest implements SequenceListener,
+ VetoableSequenceListener,
+ AlignmentListener,
+ VetoableAlignmentListener
+{
+ private SequenceAlignmentTest()
+ {
+ // print header...
+ System.out.println("-= SequenceAlignmentTest =-");
+ System.out.println("\nTesting the sequence alignment class, and the events\n");
+
+ // generate sequences of elements
+ Element[][] elems = new Element[3][];
+ elems[0] = new Element[] {
+ AminoAcid.ALANINE,
+ AminoAcid.ARGININE,
+ AminoAcid.ASPARAGINE,
+ AminoAcid.ASPARTICACID,
+ AminoAcid.CYSTEINE,
+ AminoAcid.GLUTAMICACID,
+ AminoAcid.GLUTAMINE,
+ AminoAcid.GLYCINE,
+ AminoAcid.HISTIDINE,
+ AminoAcid.ISOLEUCINE,
+ AminoAcid.LEUCINE,
+ AminoAcid.LYSINE,
+ AminoAcid.METHIONINE,
+ AminoAcid.PHENYLALANINE,
+ AminoAcid.SERINE,
+ AminoAcid.THREONINE,
+ AminoAcid.TYROSINE,
+ AminoAcid.TRYPTOPHAN,
+ AminoAcid.VALINE
+ };
+ elems[1] = AminoAcid.getAll();
+ elems[2] = new Element[] {
+ AminoAcid.VALINE,
+ AminoAcid.PROLINE,
+ AminoAcid.METHIONINE,
+ AminoAcid.ALANINE
+ };
+ System.out.println("\ngenerated sequences of elements. The lengths are:");
+ for (int i = 0; i < elems.length; i++) {
+ System.out.print(" " + Integer.toString(elems[i].length));
+ }
+ System.out.print("\n");
+
+ // generate sequences from elems array
+ DefaultGappedSequence seqs[] = new DefaultGappedSequence[elems.length];
+ for (int i = 0; i < seqs.length; i++) {
+ seqs[i] = new DefaultGappedSequence
+ (elems[i], ProteinSequenceType.getInstance());
+ }
+ System.out.println("\ngenerated sequences:");
+ for (int i = 0; i < seqs.length; i++) {
+ System.out.println(" " + String.valueOf(seqs[i].getSequenceAsChars()));
+ }
+
+ // make sequences all same length
+ int max_seq_length = 0;
+ for (int i = 0; i < seqs.length; i++) {
+ if (max_seq_length < seqs[i].getGappedLength())
+ max_seq_length = seqs[i].getGappedLength();
+ }
+ for (int i = 0; i < seqs.length; i++) {
+ if ((max_seq_length - seqs[i].getGappedLength()) > 0) {
+ try {
+ seqs[i].insertGapAt((seqs[i].getGappedLength() + 1),
+ (max_seq_length - seqs[i].getGappedLength()));
+ } catch (SequenceVetoException e) {
+ System.out.println(" caught sequence veto exception with " +
+ "sequence " + Integer.toString(i) + ".");
+ e.printStackTrace();
+ }
+ }
+ }
+ System.out.println("\nsequences lengthened and now read:");
+ for (int i = 0; i < seqs.length; i++) {
+ System.out.println(" " + String.valueOf(seqs[i].getGappedSequenceAsChars()));
+ }
+
+ // generate msa
+ DefaultSequenceAlignment msa = new DefaultSequenceAlignment
+ (seqs, ProteinSequenceType.getInstance());
+ System.out.println("\ngenerated a sequence alignment (type: " +
+ msa.getSequenceType() + ") of the " +
+ Integer.toString(msa.getNumberSequences()) +
+ " sequences, ");
+ System.out.println("which makes the msa " +
+ Integer.toString(msa.getLength()) +
+ " elements long...");
+ System.out.println("sequence at index 3: " +
+ Sequences.getGappedSequenceAsString
+ ((msa.getSequenceAt(3))));
+ System.out.println(" reverse using getSequenceIndex: " +
+ Integer.toString(msa.getSequenceIndex
+ (msa.getSequenceAt(3))));
+
+
+ // generating a sub-alignment
+ System.out.println("\ngetting a sub-alignment [3,10,1,3]...");
+ DefaultSequenceAlignment submsa = (DefaultSequenceAlignment)
+ msa.getSubAlignment(3, 10, 1, 3);
+ for (int i = 0; i < submsa.getNumberSequences(); i++) {
+ System.out.println(" " + Sequences.getGappedSequenceAsString
+ (submsa.getSequenceAt(i + 1)));
+ }
+
+ Sequences.printAlignment( submsa );
+
+ // become a listener of the alignment
+ msa.addAlignmentListener(this);
+ System.out.println("\nadded myself as a listener of the MSA...");
+
+ System.out.println("\nsetting inset on sequence 1 of 3...");
+ try {
+ msa.setInset(1, 3);
+ } catch (AlignmentVetoException e) {
+ System.out.print(" EXCEPTION: Alignment veto exception was thrown and caught\n" +
+ " ");
+ e.printStackTrace();
+ System.exit(1);
+ }
+
+ // print out msa, with '_' representing inset's
+ System.out.println("msa now:");
+ for (int i = 0; i < msa.getNumberSequences(); i++) {
+ System.out.print(" ");
+ for (int j = 0; j < msa.getInset(i + 1); j++)
+ System.out.print("_");
+ System.out.println(Sequences.getGappedSequenceAsString(msa.getSequenceAt(i + 1)));
+ }
+
+
+ System.out.println("\n\n-= SequenceAlignmentTest class complete =-");
+ }
+
+ public static void main(String[] args)
+ {
+ SequenceAlignmentTest sat = new SequenceAlignmentTest();
+ }
+
+ public void changeOccurred(SequenceEvent event)
+ {
+ System.out.println("\n-< a sequence event was fired to indicate a " +
+ "change >-");
+ }
+
+ public void vetoableChangeOccurred(VetoableSequenceEvent event)
+ throws SequenceVetoException
+ {
+ System.out.println("\n-< a vetoable sequence event was fired to indicate " +
+ "a change >-");
+ }
+
+ public void changeOccurred(AlignmentEvent event)
+ {
+ System.out.println("\n-< an alignment event was fired to indicate a " +
+ "change to the alignment >-");
+ }
+
+ public void vetoableChangeOccurred(VetoableAlignmentEvent event)
+ throws AlignmentVetoException
+ {
+ System.out.println("\n-< a vetoable alignment event was fired to indicate " +
+ "a change to the alignment >-");
+ }
+} // SequenceAlignmentTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignmentTest.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.3 2000/04/18 17:52:28 jns
+ * o changes madde because of files moved to types package.
+ *
+ * Revision 1.2 2000/03/21 13:14:51 jns
+ * o added listener stuff, plus a check on the get/set Inset methods.
+ *
+ * Revision 1.1 2000/03/16 17:32:56 jns
+ * initial code
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/test/SequenceColumnTest.java b/src/uk/ac/man/bioinf/sequence/test/SequenceColumnTest.java
new file mode 100644
index 0000000..f4189b9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/SequenceColumnTest.java
@@ -0,0 +1,79 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.apps.cinema.core.test.CinemaTestLaunch;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.AlignmentColumn;
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+
+
+/**
+ * SequenceColumnTest.java
+ *
+ *
+ * Created: Wed Jun 7 15:41:17 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceColumnTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceColumnTest
+{
+
+ public static void main( String[] args ) throws Throwable
+ {
+ SequenceAlignment msa = CinemaTestLaunch.generateMsa();
+
+ Sequences.printAlignment( msa );
+
+ AlignmentColumn col = new AlignmentColumn( msa );
+
+ for( int i = 1; i != msa.getLength(); i++ ){
+ System.out.print( "Column " + i + ":\t" );
+ col.setColumn( i );
+ for( int j = 1; j < msa.getNumberSequences(); j++ ){
+ System.out.print( col.getElementAtRow( j ).toChar() );
+ }
+ System.out.println();
+ }
+ } //end main method
+} // SequenceColumnTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceColumnTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/06/13 11:02:29 lord
+ * Boring changes
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.java b/src/uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.java
new file mode 100644
index 0000000..78f392c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/SequenceFactoryTest.java
@@ -0,0 +1,85 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Sequence;
+import uk.ac.man.bioinf.sequence.SequenceFactory;
+import uk.ac.man.bioinf.sequence.Sequences;
+
+
+/**
+ * SequenceFactoryTest.java
+ *
+ *
+ * Created: Tue Nov 14 18:21:42 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceFactoryTest.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceFactoryTest
+{
+
+ public static void main( String[] args )
+ {
+ char[] cProtSeq = { 'c','d','e','f','g','h','i','k','l'
+ };
+
+ Sequence protSeq = SequenceFactory.getProteinSequence
+ ( cProtSeq );
+
+ Sequences.printSequence( protSeq );
+
+
+ char[] cDNASeq = { 'c','a','g','a','a','c','c','c','a','g','t','t','c','c','c','t'
+ };
+
+ Sequence dnaSeq = SequenceFactory.getDNASequence
+ ( cDNASeq );
+
+ Sequences.printSequence( dnaSeq );
+
+
+
+ } //end main method
+
+
+} // SequenceFactoryTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceFactoryTest.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/27 18:14:59 lord
+ * *** empty log message ***
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/test/SequencesTest.java b/src/uk/ac/man/bioinf/sequence/test/SequencesTest.java
new file mode 100644
index 0000000..62b209e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/test/SequencesTest.java
@@ -0,0 +1,104 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.test; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.*;
+import uk.ac.man.bioinf.sequence.Sequences;
+import uk.ac.man.bioinf.sequence.alignment.Gap;
+import uk.ac.man.bioinf.sequence.types.AminoAcid;
+import uk.ac.man.bioinf.sequence.types.ProteinSequenceType;
+import uk.ac.man.bioinf.sequence.Element;
+
+/**
+ * SequencesTest.java
+ *
+ *
+ * Created: Tue Mar 14 14:19:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequencesTest.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequencesTest
+{
+
+ public static void main( String[] args )
+ {
+ // generate sequences of elements
+
+ Element[] elems = {
+ Gap.GAP,
+ AminoAcid.ALANINE,
+ AminoAcid.ARGININE,
+ AminoAcid.ASPARAGINE,
+ AminoAcid.ASPARTICACID,
+ AminoAcid.CYSTEINE,
+ Gap.GAP,
+ AminoAcid.GLUTAMICACID,
+ AminoAcid.GLUTAMINE,
+ AminoAcid.GLYCINE,
+ AminoAcid.HISTIDINE,
+ AminoAcid.ISOLEUCINE,
+ AminoAcid.LEUCINE,
+ AminoAcid.LYSINE,
+ AminoAcid.METHIONINE,
+ Gap.GAP,
+ AminoAcid.PHENYLALANINE,
+ AminoAcid.SERINE,
+ AminoAcid.THREONINE,
+ AminoAcid.TYROSINE,
+ AminoAcid.TRYPTOPHAN,
+ AminoAcid.VALINE,
+ Gap.GAP
+ };
+
+ Sequences.printSequence( Sequences.getElementsAsGappedSequence( elems, ProteinSequenceType.getInstance() ) );
+ } //end main method
+
+
+} // SequencesTest
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequencesTest.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/06/23 12:57:59 jns
+ * o added in the Sequences import - it wasn't compiling.
+ *
+ * Revision 1.2 2000/04/18 17:52:28 jns
+ * o changes madde because of files moved to types package.
+ *
+ * Revision 1.1 2000/03/16 16:17:40 lord
+ * Initial checkin
+ *
+*/
diff --git a/src/uk/ac/man/bioinf/sequence/types/AbstractElement.java b/src/uk/ac/man/bioinf/sequence/types/AbstractElement.java
new file mode 100644
index 0000000..13c1ecf
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/AbstractElement.java
@@ -0,0 +1,102 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.util.AbstractEnumeration;
+import uk.ac.man.bioinf.sequence.Element;
+
+
+/**
+ * AbstractElement.java
+ *
+ *
+ * Created: Mon Feb 28 16:10:45 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractElement.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractElement extends AbstractEnumeration
+{
+ private char toChar;
+
+ public AbstractElement( String toString, char toChar )
+ {
+ super( toString );
+ this.toChar = toChar;
+ }
+
+ public char toChar()
+ {
+ return toChar;
+ }
+
+ /**
+ * Returns all the elements. This method basically switches the type
+ * of the
+ * @param cla the class of the elements
+ * @return the Elements of the class
+ */
+ public static Element[] getAllSequenceElements( Class cla )
+ {
+ AbstractEnumeration[] enum = AbstractEnumeration.getAllElements( cla );
+
+ Element[] elems = new Element[ enum.length ];
+
+ System.arraycopy( enum, 0, elems, 0, elems.length );
+
+ return elems;
+ }
+} // AbstractElement
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractElement.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.2 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/02/28 16:32:39 lord
+ * Numerous changes
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.java b/src/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.java
new file mode 100644
index 0000000..271fc5e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/AbstractEnumeratedSequenceType.java
@@ -0,0 +1,85 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.types.AbstractElement;
+
+
+/**
+ * AbstractEnumeratedSequenceType.java
+ *
+ *
+ * Created: Tue Jun 13 13:20:11 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractEnumeratedSequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class AbstractEnumeratedSequenceType extends AbstractSequenceType
+{
+
+ public AbstractEnumeratedSequenceType( Element[] elements, String name )
+ {
+ super( elements, name );
+ }
+
+ public AbstractEnumeratedSequenceType( Element[][] elements, String name )
+ {
+ super( elements, name );
+ }
+
+ public int getIntForElement( Element element )
+ {
+ if( !isElement( element ) )
+ // (PENDING:- PL) This should be a more specific exception
+ throw new IllegalArgumentException( "Element is not a member of the sequence type " + this );
+
+ // we know that this is going to be a AbstractElement because the
+ // constructor requires it
+ return ((AbstractElement)element).ord;
+ }
+
+ public Element getElementForInt( int index )
+ {
+ return elements[ index ];
+ }
+} // AbstractEnumeratedSequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractEnumeratedSequenceType.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/06/27 16:12:15 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.java b/src/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.java
new file mode 100644
index 0000000..c2deba1
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/AbstractSequenceType.java
@@ -0,0 +1,168 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.SequenceType;
+import uk.ac.man.bioinf.sequence.Element;
+
+/**
+ * AbstractSequenceType.java
+ *
+ *
+ * Created: Thu Feb 17 13:02:28 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractSequenceType.java,v 1.5 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractSequenceType implements SequenceType
+{
+ private String name;
+ protected Element[] elements;
+
+ public AbstractSequenceType( Element[] elements, String name )
+ {
+ init( elements, name );
+ }
+
+ public AbstractSequenceType( Element[][] elements, String name )
+ {
+ int count = 0;
+ for( int i = 0; i < elements.length; i++ ){
+ count += elements[ i ].length;
+ }
+ Element[] allElements = new Element[ count ];
+
+ int pos = 0;
+ for( int i = 0; i < elements.length; i++ ){
+ System.arraycopy( elements[ i ], 0, allElements, pos, elements[ i ].length );
+ pos = elements[ i ].length;
+ }
+ init( allElements, name );
+ }
+
+ private void init( Element[] elements, String name )
+ {
+ this.elements = elements;
+ this.name = name;
+ }
+
+ // PENDING Should improve these implementations I think. Is a hash
+ // table worth it? Depends on how many Elements I Guess...
+ public boolean isElement( Element element )
+ {
+ for( int i = 0; i < elements.length; i ++ ){
+ if( elements[ i ] == element ) return true;
+ }
+ return false;
+ }
+
+ public boolean isElement( Element[] element )
+ {
+ for( int i = 0 ; i < element.length ; i++ ){
+ if( !isElement( element[ i ] ) ) return false;
+ } //end for( i < Element.length )
+ return true;
+ }
+
+ public boolean isElement( char element )
+ {
+ for( int i = 0 ; i < elements.length ; i++ ){
+ if( elements[ i ].toChar() == element ) return true;
+ } //end for( i < elements.length )
+ return false;
+ }
+
+ public boolean isElement( char[] element )
+ {
+ for( int i = 0 ; i < element.length ; i++ ){
+ if( !isElement( element[ i ] ) ) return false;
+ } //end for( i < element.length )
+ return false;
+ }
+
+ public String getName()
+ {
+ if( name == null ) throw new IllegalStateException
+ ( "The name of an AbstractSequenceType should be set during construction" );
+ return name;
+ }
+
+ public Element[] getElements()
+ {
+ if( elements == null ) throw new IllegalStateException
+ ( "The Elements of an AbstractSequenceType should be set during construction" );
+ return (Element[])elements.clone();
+ }
+
+ public int size()
+ {
+ return elements.length;
+ }
+} // AbstractSequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractSequenceType.java,v $
+ * Revision 1.5 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.4 2000/08/01 12:47:05 jns
+ * o removed references to BioInterface and BioObject.
+ *
+ * Revision 1.3 2000/06/27 16:12:52 lord
+ * Loosened access on internal data structures
+ *
+ * Revision 1.2 2000/06/13 11:01:59 lord
+ * Added size method
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.3 2000/03/02 17:46:52 lord
+ * Now declared abstract
+ *
+ * Revision 1.2 2000/03/01 20:17:41 lord
+ * Updated for new interfaces
+ *
+ * Revision 1.1 2000/02/28 16:32:39 lord
+ * Numerous changes
+ *
+ * Revision 1.2 2000/02/18 20:06:39 lord
+ * Implements isElement methods.
+ * Now extends BioObject rather than delegates.
+ * Removed AbstractElement reference.
+ * SequenceType name support added properly
+ *
+ * Revision 1.1 2000/02/18 18:39:57 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/AminoAcid.java b/src/uk/ac/man/bioinf/sequence/types/AminoAcid.java
new file mode 100644
index 0000000..631bc33
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/AminoAcid.java
@@ -0,0 +1,168 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Element;
+
+
+/**
+ * AminoAcid.java
+ *
+ * A class for the representation of an amino-acid. This class is an
+ * enumeration of types.
+ *
+ * Created: Wed Feb 16 20:30:57 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AminoAcid.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public final class AminoAcid extends AbstractElement
+ implements ProteinResidue
+{
+ // this is for the Element, and AminoAcid implementation.
+ private String threeLetter;
+ private String full;
+
+ private AminoAcid( char singleChar, String threeLetter, String full, String toString )
+ {
+ super( toString, singleChar );
+ this.threeLetter = threeLetter;
+ this.full = full;
+ }
+
+ public String getThreeLetter()
+ {
+ return threeLetter;
+ }
+
+ public String getFullName()
+ {
+ return full;
+ }
+
+ public static AminoAcid[] getAll()
+ {
+ Element[] elems = getAllSequenceElements( AminoAcid.class );
+
+ AminoAcid[] aa = new AminoAcid[ elems.length ];
+
+ System.arraycopy( elems, 0, aa, 0, elems.length );
+
+ return aa;
+ }
+
+
+ // static types.
+ public static final AminoAcid GLYCINE =
+ new AminoAcid( 'G', "Gly", "Glycine", "AminoAcid Glycine" );
+ public static final AminoAcid ALANINE =
+ new AminoAcid( 'A', "Ala", "Alanine", "AminoAcid Alanine" );
+ public static final AminoAcid VALINE =
+ new AminoAcid( 'V', "Val", "Valine", "AminoAcid Valine" );
+ public static final AminoAcid LEUCINE =
+ new AminoAcid( 'L', "Leu", "Leucine", "AminoAcid Leucine" );
+ public static final AminoAcid ISOLEUCINE =
+ new AminoAcid( 'I', "Ile", "Isoleucine", "AminoAcid IsoLeucine" );
+ public static final AminoAcid SERINE =
+ new AminoAcid( 'S', "Ser", "Serine", "AminoAcid Serine" );
+ public static final AminoAcid CYSTEINE =
+ new AminoAcid( 'C', "Cys", "Cysteine", "AminoAcid Cysteine" );
+ public static final AminoAcid THREONINE =
+ new AminoAcid( 'T', "Thr", "Threonine", "AminoAcid Threonine" );
+ public static final AminoAcid METHIONINE =
+ new AminoAcid( 'M', "Met", "Methonine", "AminoAcid Methonine" );
+ public static final AminoAcid PHENYLALANINE =
+ new AminoAcid( 'F', "Phe", "Phenylalanine", "AminoAcid Phenylalanine" );
+ public static final AminoAcid TYROSINE =
+ new AminoAcid( 'Y', "Tyr", "Tyrosine", "AminoAcid Tyrosine" );
+ public static final AminoAcid TRYPTOPHAN =
+ new AminoAcid( 'W', "Trp", "Tryptophan", "AminoAcid Tryptophan" );
+ public static final AminoAcid PROLINE =
+ new AminoAcid( 'P', "Pro", "Proline", "AminoAcid Proline" );
+ public static final AminoAcid HISTIDINE =
+ new AminoAcid( 'H', "His", "Histidine", "AminoAcid Histidine" );
+ public static final AminoAcid LYSINE =
+ new AminoAcid( 'K', "Lys", "Lysine", "AminoAcid Lysine" );
+ public static final AminoAcid ARGININE =
+ new AminoAcid( 'R', "Arg", "Arginine", "AminoAcid Arginine" );
+ public static final AminoAcid ASPARTICACID =
+ new AminoAcid( 'D', "Asp", "AsparticAcid", "AminoAcid AsparticAcid" );
+ public static final AminoAcid GLUTAMICACID =
+ new AminoAcid( 'E', "Glu", "GlutamicAcid", "AminoAcid GlutamicAcid" );
+ public static final AminoAcid ASPARAGINE =
+ new AminoAcid( 'N', "Asn", "Asparagine", "AminoAcid Asparagine" );
+ public static final AminoAcid GLUTAMINE =
+ new AminoAcid( 'Q', "Gln", "Glutamine", "AminoAcid Glutamine" );
+ public static final AminoAcid ASNORASP =
+ new AminoAcid( 'B', "Asx", "Asparagine or AsparticAcid", "AminoAcid Asn or Asp" );
+ public static final AminoAcid GLUORGLN =
+ new AminoAcid( 'Z', "Glx", "GlutamicAcid or Glutamine", "Amino Acid Glu or Gln" );
+ public static final AminoAcid ANY =
+ new AminoAcid( 'X', "Any", "Any", "AminoAcid any" );
+} // AminoAcid
+
+
+
+/*
+ * ChangeLog
+ * $Log: AminoAcid.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/04/06 13:17:33 lord
+ * Added ambiguity types
+ *
+ * Revision 1.4 2001/03/15 13:20:25 lord
+ * Fixed bug in Threonine toString() parameter
+ *
+ * Revision 1.3 2000/07/18 12:39:06 lord
+ * Import rationalisation
+ *
+ * Revision 1.2 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.4 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ * Revision 1.3 2000/02/28 16:32:39 lord
+ * Numerous changes
+ *
+ * Revision 1.2 2000/02/28 16:20:07 lord
+ * FIxed typo
+ *
+ * Revision 1.1 2000/02/28 14:07:16 jns
+ * Initial code, although will not currently compile due to certain files
+ * not being present, such as AbstractSequenceType, and AbstractEnumeration.
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/DNANucleotide.java b/src/uk/ac/man/bioinf/sequence/types/DNANucleotide.java
new file mode 100644
index 0000000..715ea2c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/DNANucleotide.java
@@ -0,0 +1,95 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Element;
+
+
+/**
+ * DNANucleotide.java
+ *
+ *
+ * Created: Sun Sep 24 17:44:04 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: DNANucleotide.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DNANucleotide extends AbstractElement
+ implements DNAResidue
+{
+ //Store the full name
+ private String full;
+ private DNANucleotide ( char singleChar, String full, String toString )
+ {
+ super( toString, singleChar );
+ this.full = full;
+ }
+
+ public String getFullName()
+ {
+ return full;
+ }
+
+ public static DNANucleotide[] getAll()
+ {
+ Element[] elems = getAllSequenceElements( DNANucleotide.class );
+ DNANucleotide[] dna = new DNANucleotide[ elems.length ];
+
+ System.arraycopy( elems, 0, dna, 0, dna.length );
+ return dna;
+ }
+
+ public static final DNANucleotide ADENOSINE =
+ new DNANucleotide('A', "Adenosine", "DNANucleotide Adenosine");
+ public static final DNANucleotide GUANINE =
+ new DNANucleotide('G', "Guanine", "DNANucleotide Guanine");
+ public static final DNANucleotide CYTOSINE =
+ new DNANucleotide('C', "Cytosine", "DNANucleotide Cytosine");
+ public static final DNANucleotide THIAMINE =
+ new DNANucleotide('T', "Thiamine", "DNANucleotide Thiamine");
+
+
+
+} // DNANucleotide
+
+
+
+/*
+ * ChangeLog
+ * $Log: DNANucleotide.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/27 18:16:19 lord
+ * Amusingly I had Uracil as one of the DNA
+ *
+ * Revision 1.1 2000/09/25 16:37:38 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/DNAResidue.java b/src/uk/ac/man/bioinf/sequence/types/DNAResidue.java
new file mode 100644
index 0000000..3836b5e
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/DNAResidue.java
@@ -0,0 +1,65 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+
+/**
+ * DNAResidue.java
+ *
+ * An interface to represent a DNA residue.
+ *
+ * Created: Mon Feb 28 13:02:09 2000
+ *
+ * @author J Selley
+ * @version $Id: DNAResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface DNAResidue extends NucleotideResidue
+{
+
+}// DNAResidue
+
+
+/*
+ * ChangeLog
+ * $Log: DNAResidue.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.2 2000/03/02 17:25:22 jns
+ * removal of NucleotideReside class and change of DNA Residue to extend
+ * NucleotideResidue rather than the fore mentioned.
+ *
+ * Revision 1.1 2000/02/28 14:04:37 jns
+ * Initial code.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/types/DNASequenceType.java b/src/uk/ac/man/bioinf/sequence/types/DNASequenceType.java
new file mode 100644
index 0000000..3888cfd
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/DNASequenceType.java
@@ -0,0 +1,73 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+
+/**
+ * DNASequenceType.java
+ *
+ * This class represents the DNA sequence type, allowing only a set
+ * of particular bases.
+ *
+ * Created: Tue Aug 22 18:41:00 2000
+ *
+ * @author Julian Selley
+ * @version $Id: DNASequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class DNASequenceType extends AbstractEnumeratedSequenceType
+{
+ private DNASequenceType()
+ {
+ super(AbstractElement.getAllSequenceElements(DNANucleotide.class),
+ "DNASequenceType");
+ }
+
+ public static final DNASequenceType instance = new DNASequenceType();
+
+ public static DNASequenceType getInstance()
+ {
+ return instance;
+ }
+} // DNASequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: DNASequenceType.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/11/15 14:35:15 lord
+ * Updated due to removal of DNABase class
+ *
+ * Revision 1.1 2000/09/18 12:49:54 jns
+ * o Initial commit. Needed for EMBOSS.
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/EmptySequenceType.java b/src/uk/ac/man/bioinf/sequence/types/EmptySequenceType.java
new file mode 100644
index 0000000..441a456
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/EmptySequenceType.java
@@ -0,0 +1,115 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Element;
+import uk.ac.man.bioinf.sequence.SequenceType;
+
+
+/**
+ * EmptySequenceType.java
+ *
+ *
+ * Created: Tue Aug 1 17:22:00 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: EmptySequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class EmptySequenceType implements SequenceType
+{
+ public static final EmptySequenceType INSTANCE = new EmptySequenceType();
+
+ private EmptySequenceType()
+ {
+ }
+
+ public static SequenceType getInstance()
+ {
+ return INSTANCE;
+ }
+
+ public int size()
+ {
+ return 0;
+ }
+
+ public int getIntForElement( Element element )
+ {
+ throw new IllegalArgumentException( "EmptySequenceType has no elements to convert to an int" );
+ }
+
+
+ public Element getElementForInt( int index )
+ {
+ return null;
+ }
+
+ public Element[] getElements()
+ {
+ return new Element[ 0 ];
+ }
+
+ public String getName()
+ {
+ return "EmptySequenceType";
+ }
+
+ public boolean isElement(char element)
+ {
+ return false;
+ }
+
+ public boolean isElement(Element element)
+ {
+ return false;
+ }
+
+ public boolean isElement(char[] elements)
+ {
+ return false;
+ }
+
+ public boolean isElement(Element[] elements)
+ {
+ return false;
+ }
+} // EmptySequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: EmptySequenceType.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/08/01 17:18:53 lord
+ * Intial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/NucleotideResidue.java b/src/uk/ac/man/bioinf/sequence/types/NucleotideResidue.java
new file mode 100644
index 0000000..d729bd9
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/NucleotideResidue.java
@@ -0,0 +1,66 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Residue;
+
+
+/**
+ * NucleotideResidue.java
+ *
+ * An interface to mark up nucleotide residues.
+ *
+ * Created: Mon Feb 28 12:59:40 2000
+ *
+ * @author J Selley
+ * @version $Id: NucleotideResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface NucleotideResidue extends Residue
+{
+
+}// NucleotideResidue
+
+
+/*
+ * ChangeLog
+ * $Log: NucleotideResidue.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.1 2000/02/28 16:32:39 lord
+ * Numerous changes
+ *
+ * Revision 1.1 2000/02/28 14:05:34 jns
+ * Initial code.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/types/ProteinResidue.java b/src/uk/ac/man/bioinf/sequence/types/ProteinResidue.java
new file mode 100644
index 0000000..a297431
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/ProteinResidue.java
@@ -0,0 +1,73 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Julian Selley (j.selley at man.ac.uk)
+ * whilst at the University of Manchester as a Research Assistant.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.Residue;
+
+
+/**
+ * ProteinResidue.java
+ *
+ * An interface to represent a protein residue.
+ *
+ * Created: Mon Feb 28 13:08:13 2000
+ *
+ * @author J Selley
+ * @version $Id: ProteinResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ProteinResidue extends Residue
+{
+
+}// ProteinResidue
+
+
+/*
+ * ChangeLog
+ * $Log: ProteinResidue.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.2 2000/03/01 20:17:41 lord
+ * Updated for new interfaces
+ *
+ * Revision 1.1 2000/02/28 14:05:53 jns
+ * Initial code.
+ *
+ */
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.java b/src/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.java
new file mode 100644
index 0000000..022e77b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/ProteinSequenceType.java
@@ -0,0 +1,78 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+
+
+/**
+ * ProteinSequenceType.java
+ *
+ *
+ * Created: Fri Mar 3 16:12:39 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ProteinSequenceType.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ProteinSequenceType extends AbstractEnumeratedSequenceType
+{
+ private ProteinSequenceType()
+ {
+ super( AbstractElement.getAllSequenceElements( AminoAcid.class ),
+ "ProteinSequenceType" );
+ }
+
+ public static final ProteinSequenceType instance = new ProteinSequenceType();
+
+ public static ProteinSequenceType getInstance()
+ {
+ return instance;
+ }
+} // ProteinSequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: ProteinSequenceType.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/07/18 12:39:21 lord
+ * Import rationalisation
+ * Changes due to BioInterface removal
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.1 2000/03/08 17:26:35 lord
+ * To many changes to document
+ *
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/sequence/types/RNANucleotide.java b/src/uk/ac/man/bioinf/sequence/types/RNANucleotide.java
new file mode 100644
index 0000000..51b012d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/RNANucleotide.java
@@ -0,0 +1,105 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Daniel Jameson (daniel.p.jameson at stud.man.ac.uk)
+ * whilst at the University of Manchester as a Masters Student.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+import uk.ac.man.bioinf.sequence.Element;
+
+
+
+/**
+ * RNANucleotide.java
+ *
+ * A class for the representation of RNA Nucleotides. This class
+ * is an enumeration of types.
+ *
+ * Created: Mon Feb 28 15:42:47 2000
+ *
+ * @author Daniel Jameson
+ * @version $Id: RNANucleotide.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public final class RNANucleotide extends AbstractElement
+ implements RNAResidue
+{
+ //Store the full name
+ private String full;
+ private RNANucleotide ( char singleChar, String full, String toString )
+ {
+ super( toString, singleChar );
+ this.full = full;
+ }
+
+ public String getFullName()
+ {
+ return full;
+ }
+
+ public static RNANucleotide[] getAll()
+ {
+ Element[] elems = getAllSequenceElements( RNANucleotide.class );
+ RNANucleotide[] rna = new RNANucleotide[ elems.length ];
+
+ System.arraycopy( elems, 0, rna, 0, rna.length );
+ return rna;
+ }
+
+ public static final RNANucleotide ADENOSINE =
+ new RNANucleotide('A', "Adenosine", "RNANucleotide Adenosine");
+ public static final RNANucleotide GUANINE =
+ new RNANucleotide('G', "Guanine", "RNANucleotide Guanine");
+ public static final RNANucleotide CYTOSINE =
+ new RNANucleotide('C', "Cytosine", "RNANucleotide Cytosine");
+ public static final RNANucleotide URACIL =
+ new RNANucleotide('U', "Uracil", "RNANucleotide Uracil");
+} // RNANucleotide
+
+
+
+/*
+ * ChangeLog
+ * $Log: RNANucleotide.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/05/30 16:04:18 lord
+ * Have rationalised and sorted all the import statements
+ *
+ * Revision 1.2 2000/05/10 15:00:26 lord
+ * Get all elements support added
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.2 2000/02/28 16:32:39 lord
+ * Numerous changes
+ *
+ * Revision 1.1 2000/02/28 16:06:36 jameson
+ * Initial checkin.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/types/RNAResidue.java b/src/uk/ac/man/bioinf/sequence/types/RNAResidue.java
new file mode 100644
index 0000000..fe736b7
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/RNAResidue.java
@@ -0,0 +1,62 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Daniel Jameson (daniel.p.jameson at stud.man.ac.uk)
+ * whilst at the University of Manchester as a Masters Student.
+ *
+ * The initial code base is copyright by the University of Manchester.
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate. Authorship
+ * of the modifications may be determined from the ChangeLog placed
+ * at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+/**
+ * RNAResidue.java
+ *
+ * An interface to represent an RNA Residue
+ *
+ * Created: Mon Feb 28 13:02:16 2000
+ *
+ * @author Daniel Jameson
+ * @version $Id: RNAResidue.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface RNAResidue extends NucleotideResidue
+{
+}// RNAResidue
+
+
+/*
+ * ChangeLog
+ * $Log: RNAResidue.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/04/18 17:54:48 jns
+ * o files previously in sequence package, moved here.
+ *
+ * Revision 1.2 2000/02/28 16:32:39 lord
+ * Numerous changes
+ *
+ * Revision 1.1 2000/02/28 15:40:46 jameson
+ * Initial checkin.
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/sequence/types/RNASequenceType.java b/src/uk/ac/man/bioinf/sequence/types/RNASequenceType.java
new file mode 100644
index 0000000..a5d458b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/sequence/types/RNASequenceType.java
@@ -0,0 +1,71 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.sequence.types; // Package name inserted by JPack
+
+
+/**
+ * RNASequenceType.java
+ *
+ *
+ * Created: Mon Nov 27 16:02:20 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: RNASequenceType.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class RNASequenceType extends AbstractEnumeratedSequenceType
+{
+
+ public RNASequenceType()
+ {
+ super(AbstractElement.getAllSequenceElements(RNANucleotide.class),
+ "RNASequenceType");
+
+ }
+
+ public static final RNASequenceType instance = new RNASequenceType();
+
+ public static RNASequenceType getInstance()
+ {
+ return instance;
+ }
+} // RNASequenceType
+
+
+
+/*
+ * ChangeLog
+ * $Log: RNASequenceType.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/11/27 18:16:30 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/AbstractEnumeration.java b/src/uk/ac/man/bioinf/util/AbstractEnumeration.java
new file mode 100644
index 0000000..c9cb0a0
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/AbstractEnumeration.java
@@ -0,0 +1,286 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.NoSuchElementException;
+import java.util.ConcurrentModificationException;
+
+
+/**
+ * AbstractEnumeration.java
+ *
+ * Provides support for Enumerated Types in Java. This class provides
+ * several methods useful for all Enumerated Types including a
+ * sensible printable toString method, the total
+ * number of instances of a given type, an Iterator through all the
+ * types, and an ordinal number running from 0 upwards for each type. <p>
+ *
+ * This class is used by extending it with a new class which
+ * <ul>
+ * <li>is declared final, which prevents subclasses from
+ * introducing new instances</li>
+ * <li>has a private constructor</li>
+ * <li>declares a public static final data member for each instance
+ * that is required</li>
+ * </ul>
+ *
+ * So for example
+ *
+ * <code>
+ * <pre>
+ * public final class TrafficLight extends AbstractEnumeration
+ * {
+ * private TrafficLight( String toString ){
+ * {
+ * super( toString );
+ * }
+ *
+ * public static final TrafficLight RED
+ * = new TrafficLight( "TrafficLight Enumerated Type:- RED" );
+ * public static final TrafficLight ORANGE
+ * = new Traffic( "TrafficLight Enumerated Type:- ORANGE" );
+ * public static final TrafficLight GREEN
+ * = new Traffic( TrafficLight Enumerated Type:- GREEN" );
+ * }
+ *
+ * </pre>
+ * </code>
+ *
+ * Currently this class can not be serialised. Having one of the
+ * subclasses implement Serializable would be a mistake as it would
+ * provide an alternative route for the instances of the class to be
+ * produced. This could be circumvented using the
+ * replaceObject/writeObject methods introduced in the 1.2
+ * serialisation spec, but I haven't got around to implementing this
+ * yet!
+ *
+ * It should be noted that there are problems in compiling this class
+ * with some versions of javac. This is bug in javac (Bug ID:4157676),
+ * not my code which is perfectly legal java. Jikes works
+ * fine. Alternatively you can comment out the references to the ord
+ * variable and do without this functionality, or make it non final,
+ * in which case attempts to alter it will no longer produce compiler
+ * errors as they should.
+ *
+ * Created: Mon Feb 21 14:11:41 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: AbstractEnumeration.java,v 1.9 2001/04/11 17:04:43 lord Exp $
+ */
+
+public abstract class AbstractEnumeration
+{
+ // A linked list of all these types.
+ private String toString;
+ private AbstractEnumeration next;
+ private AbstractEnumeration prev;
+
+ // private static hashtables, which support the enum
+ // implementation. We are using hashtables because they are
+ // synchronized and they need to be for this!
+ private static Hashtable upperBoundHash = new Hashtable();
+ private static Hashtable firstHash = new Hashtable();
+ private static Hashtable lastHash = new Hashtable();
+ private static Hashtable currentTopOrd = new Hashtable();
+
+
+ // ordinal number. Very useful.
+ public final int ord; //if this does not compile its a bug in javac. Removing "final" should make it work!!!!
+
+ protected AbstractEnumeration( String toString )
+ {
+ super();
+
+ this.toString = toString;
+
+ // sort the ordinal number for this type.
+ // first retrieve it (if it exists) from the hash
+ Object upBound = upperBoundHash.get( getClass() );
+ int upperBound;
+
+ if( upBound == null ){
+ upperBound = 0;
+ }
+ else{
+ upperBound = ((Integer)upBound).intValue();
+ }
+
+ // make the upper bound recoverable. Sadly this causes javac to
+ // croak, due to a bug in javac (see for instance Bug ID:
+ // 4157676). As this utility is vital to the class I have decided
+ // to incorporate it anyway, and simply compile with Jikes. The
+ // bug should be fixed as of the 1.3 release.
+ ord = upperBound;
+ // then return the advanced upper bound to the hash
+ upperBoundHash.put( getClass(), new Integer( ++upperBound ) );
+
+
+ // next step is to make add to (or create) a linked list
+ // start and end elements in the appropriate elements
+ Object firstObj = firstHash.get( getClass() );
+ Object lastObj = lastHash.get( getClass() );
+
+ AbstractEnumeration first = (firstObj == null)? null:((AbstractEnumeration)firstObj);
+ AbstractEnumeration last = (lastObj == null)? null:((AbstractEnumeration)lastObj);
+
+ // sort out the linked list that we use to store all of the
+ // Elements
+ if( first == null ){
+ first = this;
+ firstHash.put( getClass(), first );
+ }
+
+ if( last != null ){
+ this.prev = last;
+ last.next = this;
+ }
+
+ last = this;
+ lastHash.put( getClass(), last );
+ }
+
+ // these methods are enum support
+ public static Iterator iterator( Class cla )
+ {
+ return new ElementIterator( cla );
+ }
+
+ public static class ElementIterator implements Iterator
+ {
+ // we need to store the size so that we can detect any concurrent
+ // modifications. This should only happen if things go badly
+ // wrong.
+ int size;
+
+ //store the current position
+ private AbstractEnumeration curr;
+
+ public ElementIterator( Class cla )
+ {
+ //store the size of this enum
+ size = ((Integer)upperBoundHash.get( cla )).intValue();
+
+ //store the current element
+ curr = (AbstractEnumeration)firstHash.get( cla );
+ }
+
+ public boolean hasNext()
+ {
+ if( curr != null ) return true;
+
+ return false;
+ }
+
+ public Object next()
+ {
+ if( getSize( curr.getClass() ) != size ) throw new ConcurrentModificationException
+ ( "The total number of elements has changed, which means bad things" );
+
+ if( curr == null ) throw new NoSuchElementException
+ ( "Attempt to iterate past last Element" );
+ AbstractEnumeration retn = curr;
+ curr = curr.next;
+ return retn;
+ }
+
+ public void remove()
+ {
+ throw new UnsupportedOperationException( "Removing elements not allowed" );
+ }
+ }
+
+ public static AbstractEnumeration[] getAllElements( Class cla )
+ {
+ // should I cache these. Maybe....
+ AbstractEnumeration[] allElements = new AbstractEnumeration[ getSize( cla ) ];
+
+ Iterator iter = iterator( cla );
+ int count = 0;
+ while( iter.hasNext() ){
+ allElements[ count++ ] = (AbstractEnumeration)iter.next();
+ }
+ return allElements;
+ }
+
+ public static int getSize( Class cla )
+ {
+ return ((Integer)upperBoundHash.get( cla )).intValue();
+ }
+
+ public String toString()
+ {
+ return toString;
+ }
+} // AbstractEnumeration
+
+
+
+/*
+ * ChangeLog
+ * $Log: AbstractEnumeration.java,v $
+ * Revision 1.9 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.8 2001/02/19 17:48:20 lord
+ * Added to documentation
+ *
+ * Revision 1.7 2000/12/13 16:36:01 lord
+ * Cosmetic
+ *
+ * Revision 1.6 2000/10/31 15:51:11 lord
+ * Improved documentation
+ *
+ * Revision 1.5 2000/07/18 12:39:45 lord
+ * Documentation enhancement
+ *
+ * Revision 1.4 2000/05/15 16:17:58 lord
+ * Have made final ordinal number available for all instances.
+ * I wrote the code for this previously, but it wouldnt compile
+ * through what has turned out to be a javac bug. Now that I know that
+ * I really want this functionality I have decided to put it back in
+ * despite the inconvienience.
+ *
+ * Revision 1.3 2000/05/10 15:00:09 lord
+ * Added ordinal number support to this class.
+ * Actually I already had ordinal support but for some strange
+ * reason I had not let the world see it. What was going on in my
+ * mind at that stage eh?
+ *
+ * Revision 1.2 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ * Revision 1.1 2000/02/28 15:59:37 lord
+ * Initial Checkin
+ *
+ * Revision 1.1 2000/02/21 16:48:22 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/ArrayManipulation.java b/src/uk/ac/man/bioinf/util/ArrayManipulation.java
new file mode 100644
index 0000000..bcac6b4
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/ArrayManipulation.java
@@ -0,0 +1,106 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+import java.util.NoSuchElementException;
+
+
+/**
+ * ArrayManipulation.java
+ *
+ * Just some utility functions for manipulating arrays.
+ *
+ * Created: Thu Nov 23 14:03:06 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ArrayManipulation.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ArrayManipulation
+{
+ public static int linearSearch( Object[] array, Object key )
+ {
+ for( int i = 0; i < array.length; i++ ){
+ if( array[ i ].equals( key ) ) return i;
+ }
+
+ return -1;
+ }
+
+ public static void removeFromArray( Object[] src, Object[] dest, Object remove )
+ {
+ int index = linearSearch( src, remove );
+
+ if( index == -1 ) throw new NoSuchElementException
+ ( "The source array does not contain this object" );
+
+ // copy before the index
+ System.arraycopy( src, 0, dest, 0, index );
+
+ // copy after the index
+ System.arraycopy( src, index + 1, dest, index, dest.length - index );
+ }
+
+ public static void main( String[] args )
+ {
+ Object[] src =
+ {
+ new Integer( 0 ),
+ new Integer( 1 ),
+ new Integer( 2 ),
+ new Integer( 3 ),
+ new Integer( 4 ),
+ new Integer( 5 ),
+ new Integer( 6 ),
+ new Integer( 7 ),
+ new Integer( 8 ),
+ new Integer( 9 )
+ };
+
+ CollectionPrinter.print( src );
+
+ Object[] dest = new Object[ 9 ];
+ removeFromArray( src, dest, new Integer( 4 ) );
+ CollectionPrinter.print( dest );
+ } //end main method
+
+} // ArrayManipulation
+
+
+
+/*
+ * ChangeLog
+ * $Log: ArrayManipulation.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/12/05 15:30:52 lord
+ * Initial checkin
+ *
+ */
+
diff --git a/src/uk/ac/man/bioinf/util/Changeable.java b/src/uk/ac/man/bioinf/util/Changeable.java
new file mode 100644
index 0000000..ead3d9c
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/Changeable.java
@@ -0,0 +1,60 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+
+
+/**
+ * Changeable.java
+ *
+ *
+ * Created: Wed Jul 19 17:26:01 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: Changeable.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface Changeable
+{
+ public void addChangeListener( ChangeableListener listener );
+
+ public void removeChangeListener( ChangeableListener listener );
+} // Changeable
+
+
+
+/*
+ * ChangeLog
+ * $Log: Changeable.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/26 13:29:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/ChangeableEvent.java b/src/uk/ac/man/bioinf/util/ChangeableEvent.java
new file mode 100644
index 0000000..5f8ea43
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/ChangeableEvent.java
@@ -0,0 +1,62 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+import java.util.EventObject;
+
+
+/**
+ * ChangeableEvent.java
+ *
+ *
+ * Created: Wed Jul 19 17:29:43 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ChangeableEvent.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ChangeableEvent extends EventObject
+{
+ public ChangeableEvent( Object source )
+ {
+ super( source );
+ }
+} // ChangeableEvent
+
+
+
+/*
+ * ChangeLog
+ * $Log: ChangeableEvent.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/26 13:29:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/ChangeableListener.java b/src/uk/ac/man/bioinf/util/ChangeableListener.java
new file mode 100644
index 0000000..8e89e3b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/ChangeableListener.java
@@ -0,0 +1,59 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+
+
+/**
+ * ChangeableListener.java
+ *
+ *
+ * Created: Wed Jul 19 17:28:19 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ChangeableListener.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ChangeableListener
+{
+ public void changeOccurred( ChangeableEvent event );
+
+} // ChangeableListener
+
+
+
+/*
+ * ChangeLog
+ * $Log: ChangeableListener.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/26 13:29:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/ChangeableListenerSupport.java b/src/uk/ac/man/bioinf/util/ChangeableListenerSupport.java
new file mode 100644
index 0000000..61eaa56
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/ChangeableListenerSupport.java
@@ -0,0 +1,84 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
+
+
+/**
+ * ChangeableListenerSupport.java
+ *
+ *
+ * Created: Thu Jul 20 17:58:39 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: ChangeableListenerSupport.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class ChangeableListenerSupport
+{
+ private Set listeners = Collections.synchronizedSet( new HashSet() );
+
+ public void addChangeListener( ChangeableListener listener )
+ {
+ listeners.add( listener );
+ }
+
+ public void removeChangeListener( ChangeableListener listener )
+ {
+ listeners.remove( listener );
+ }
+
+ public void fireChangeEvent( ChangeableEvent event )
+ {
+ Iterator iter = listeners.iterator();
+
+ while( iter.hasNext() ){
+ ((ChangeableListener)iter.next()).changeOccurred( event );
+ }
+ }
+} // ChangeableListenerSupport
+
+
+
+/*
+ * ChangeLog
+ * $Log: ChangeableListenerSupport.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2000/12/05 15:54:37 lord
+ * Import rationalisation
+ *
+ * Revision 1.1 2000/07/26 13:29:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/CollectionPrinter.java b/src/uk/ac/man/bioinf/util/CollectionPrinter.java
new file mode 100644
index 0000000..5d2a2ac
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/CollectionPrinter.java
@@ -0,0 +1,86 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+import java.util.Iterator;
+import java.util.Map;
+
+
+/**
+ * CollectionPrinter.java
+ *
+ *
+ * Created: Thu Jul 20 19:47:52 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: CollectionPrinter.java,v 1.4 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class CollectionPrinter
+{
+ public static void print( Map map )
+ {
+ Iterator keyIter = map.keySet().iterator();
+
+ while( keyIter.hasNext() ){
+ Object key = keyIter.next();
+
+ System.out.println( "Key: " + key + " Value: " + map.get( key ) );
+ }
+ }
+
+ public static void print( Object[] obj )
+ {
+ System.out.println( "Printing out array " + obj );
+
+ for( int i = 0; i < obj.length; i++ ){
+ System.out.println( i + ": " + obj[ i ] );
+ }
+
+ }
+} // CollectionPrinter
+
+
+
+/*
+ * ChangeLog
+ * $Log: CollectionPrinter.java,v $
+ * Revision 1.4 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.3 2000/12/18 12:15:05 jns
+ * o getting rid of system.out.println to avoid noisy output out of debug
+ * mode
+ *
+ * Revision 1.2 2000/11/27 18:17:20 lord
+ * More methods added
+ *
+ * Revision 1.1 2000/07/26 13:29:27 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/Direction.java b/src/uk/ac/man/bioinf/util/Direction.java
new file mode 100644
index 0000000..1fed27b
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/Direction.java
@@ -0,0 +1,68 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+
+
+/**
+ * Direction.java
+ *
+ * EnumeratedType defining directions.
+ *
+ * Created: Fri Jan 19 13:18:35 2001
+ *
+ * @author Phillip Lord
+ * @version $Id: Direction.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class Direction extends AbstractEnumeration
+{
+ private Direction( String toString )
+ {
+ super( toString );
+ }
+
+
+ public static final Direction NORTH = new Direction( "Direction: North" );
+ public static final Direction EAST = new Direction( "Direction: East" );
+ public static final Direction SOUTH = new Direction( "Direction: South" );
+ public static final Direction WEST = new Direction( "Direction: West" );
+} // Direction
+
+
+
+/*
+ * ChangeLog
+ * $Log: Direction.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2001/01/19 19:50:53 lord
+ * Initial checkin
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/ExceptionHandler.java b/src/uk/ac/man/bioinf/util/ExceptionHandler.java
new file mode 100644
index 0000000..64ce3b5
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/ExceptionHandler.java
@@ -0,0 +1,65 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Middlesex working as a post-doctoral
+ * research fellow.
+ *
+ * The initial code base is copyright by Middlesex Univeristy or the
+ * Birth Defects Foundation. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+
+
+/**
+ * ExceptionHandler.java
+ *
+ * This class handles exceptions!
+ *
+ * Created: Fri May 14 14:12:58 1999
+ *
+ * @author Phillip Lord
+ * @version $Id: ExceptionHandler.java,v 1.3 2001/04/11 17:04:43 lord Exp $
+ */
+
+public interface ExceptionHandler
+{
+ public void handleException( Throwable t );
+} // ExceptionHandler
+
+
+
+/*
+ * ChangeLog
+ * $Log: ExceptionHandler.java,v $
+ * Revision 1.3 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.2 2001/01/31 18:07:30 lord
+ * Repackaged
+ *
+ * Revision 1.1 2000/05/08 16:22:10 lord
+ * Initial checkin
+ *
+ * Revision 1.1 1999-05-14 14:39:03+01 phillip2
+ * Initial revision
+ *
+ */
diff --git a/src/uk/ac/man/bioinf/util/IntArrayList.java b/src/uk/ac/man/bioinf/util/IntArrayList.java
new file mode 100644
index 0000000..86cf6d2
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/IntArrayList.java
@@ -0,0 +1,347 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+import java.util.NoSuchElementException;
+import java.util.Arrays;
+
+
+/**
+ * IntArrayList.java
+ *
+ * This class provides something akin to the ArrayList class but with
+ * all the methods typed as ints, which avoids the additional bloat of
+ * having to create an object for every containined integer.
+ *
+ * Created: Fri Mar 3 23:28:54 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: IntArrayList.java,v 1.6 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class IntArrayList
+{
+ private int size;
+ private int[] elements;
+
+ private IntArrayList( boolean dontMakeArrayWhatEverTheValueOfThisParameter )
+ {
+ }
+
+ public IntArrayList()
+ {
+ this( 10 );
+ }
+
+ public IntArrayList( int initialCapacity )
+ {
+ elements = new int[ initialCapacity ];
+ }
+
+ public void ensureCapacity( int minCapacity )
+ {
+ int oldCapacity = elements.length;
+ if( minCapacity > oldCapacity ){
+ int[] oldElements = elements;
+ int newCapacity = oldCapacity * 2;
+ if( newCapacity < minCapacity ){
+ newCapacity = minCapacity;
+ }
+
+ elements = new int[ newCapacity ];
+ System.arraycopy( oldElements, 0, elements, 0 , size );
+ }
+ }
+
+ public int size()
+ {
+ return size;
+ }
+
+ public boolean isEmpty()
+ {
+ return size == 0;
+ }
+
+ public boolean contains( int elem )
+ {
+ return indexOf( elem ) >= 0;
+ }
+
+ public int indexOf( int elem )
+ {
+ for( int i = 0; i < size; i++ ){
+ if( elem == elements[ i ] )
+ return i;
+ }
+ return -1;
+ }
+
+ public int lastIndexOf( int elem )
+ {
+ for( int i = size - 1; i >= 0; i-- ){
+ if( elem == elements[ i ] ){
+ return i;
+ }
+ }
+ return -1;
+ }
+
+ private void checkRange( int index )
+ {
+ if( index < 0 || index > size ){
+ throw new NoSuchElementException( "Attempt to access element " + index + " which doesnt exist" );
+ }
+ }
+
+ public int get( int index )
+ {
+ checkRange( index );
+ return elements[ index ];
+ }
+
+ public int set( int index, int value )
+ {
+ checkRange( index );
+
+ int old = elements[ index ];
+ elements[ index ] = value;
+ return old;
+ }
+
+ public void add( int value )
+ {
+ ensureCapacity( size + 1 );
+ elements[ size++ ] = value;
+ }
+
+ public void add( int index, int value )
+ {
+ ensureCapacity( size + 1 );
+ System.arraycopy( elements, index, elements, index + 1, size - index );
+ elements[ index ] = value;
+ size++;
+ }
+
+ public int remove( int index )
+ {
+ checkRange( index );
+
+ int old = elements[ index ];
+ // if its the last element we can ignore things otherwise
+ int moved = size - 1 - index;
+ if( moved > 0 ){
+ System.arraycopy( elements, index + 1, elements, index, size - 1 - index );
+ }
+
+ size--;
+ return old;
+ }
+
+ public int[] remove( int index, int length )
+ {
+ int to = index + length;
+ checkRange( index );
+ checkRange( to );
+
+ int[] old = new int[ length ];
+ System.arraycopy( elements, to, old, 0, length );
+ System.arraycopy( elements, to, elements, index, length );
+ return old;
+ }
+
+ public void clear()
+ {
+ size = 0;
+ }
+
+ public IntArrayList getSubList( int position, int length )
+ {
+ checkRange( position );
+ checkRange( position + length );
+
+ IntArrayList retn = new IntArrayList( true );
+
+ retn.elements = new int[length];
+ retn.size = length;
+
+ System.arraycopy( elements, position, retn.elements, 0, length );
+
+ return retn;
+ }
+
+ public int[] toArray()
+ {
+ int[] retn = new int[ size ];
+ System.arraycopy( elements, 0, retn, 0, size );
+ return retn;
+ }
+
+ /**
+ * Sort the contents of this list. Does it via a modified
+ * quicksort. Which I didnt write.
+ */
+ public void sort()
+ {
+ Arrays.sort( elements, 0, size - 1 );
+ }
+
+ /**
+ * This method performs a binary search on the list. If you choose
+ * to use this method on a list which is not guarenteed to be sorted
+ * for instance by the sort method then dealing with the results is
+ * distinctly your problem.
+ * @param key the key to search for
+ * @return the position the key is at or its insertion point.
+ * @see java.util.Arrays#binarySearch(int[],int)
+ */
+ public int binarySearch( int key )
+ {
+ /* Surprise surprise. Thought this was going to be implemented by
+ * a call to the Arrays class? Well it was going to be but sadly
+ * that doesnt allow a search ( int from, int to ). The ints of
+ * the end of the list are going to be zero, or the garbage of
+ * previous entries if the list has been shrunk (since there is no
+ * reason to zero them), so letting them into the sort would be A
+ * BAD IDEA(tm). So I blatantly plagarised the code in there (like
+ * its rocket science yeah?)
+ */
+ int low = 0;
+ int high = size - 1;
+
+ while (low <= high) {
+ int mid =(low + high)/2;
+ int midVal = elements[mid];
+
+ if (midVal < key)
+ low = mid + 1;
+ else if (midVal > key)
+ high = mid - 1;
+ else
+ return mid; // key found
+ }
+ return -(low + 1); // key not found.
+ }
+
+ /**
+ * Provides a linear search. This works even if the list is not
+ * sorted, but operates in, well linear, time.
+ * @param key the key to search for
+ * @return the index or -1 if not found
+ */
+ public int linearSearch( int key )
+ {
+ for( int i = 0; i < size; i++ ){
+ if( elements[ i ] == key ){
+ return i;
+ }
+ } //end for( i < size )
+ return -1;
+ }
+
+ public boolean equals( IntArrayList list )
+ {
+ if( size != list.size ) return false;
+
+ for( int i = 0; i < size; i++ ){
+ if( elements[ i ] != list.elements[ i ] ) return false;
+ }
+
+ return true;
+ }
+
+ public void print()
+ {
+ // This is a debug method
+
+ System.out.println( "Index\tValue" );
+ for( int i = 0; i < size; i++ ){
+ System.out.println( i + "\t" + elements[ i ] );
+ } //end for( i < elements.length )
+ }
+
+} // IntArrayList
+
+
+
+/*
+ * ChangeLog
+ * $Log: IntArrayList.java,v $
+ * Revision 1.6 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.5 2001/01/04 15:00:49 lord
+ * Fixed bug in range checking code
+ *
+ * Revision 1.4 2000/06/05 14:46:43 lord
+ * Added linear search method
+ *
+ * Revision 1.3 2000/05/18 17:01:48 lord
+ * Added toArray method
+ *
+ * Revision 1.2 2000/03/14 19:44:53 jns
+ * o sorting a problem of translation of gapped and ungapped indicies.
+ *
+ * Revision 1.1 2000/03/08 17:26:36 lord
+ * To many changes to document
+ *
+ */
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/uk/ac/man/bioinf/util/PackageResourceAdapter.java b/src/uk/ac/man/bioinf/util/PackageResourceAdapter.java
new file mode 100644
index 0000000..6dd4a57
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/PackageResourceAdapter.java
@@ -0,0 +1,55 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.util;
+import java.util.ResourceBundle;
+import java.util.Locale;
+import java.net.URL;
+import java.io.File;
+import java.io.IOException;
+/**
+ * Looks specifically for resources in the package 'resource' that should be at the route of the Application's class path.
+ * Specifically:
+ * <ul>
+ * <li> images should go in <code>resources.images</code>
+ * <li> help documentation should go in <code>resources.helpfiles</code>
+ * <li> locale data (messages, tooltips and paths to other resources such as images)
+ * should go in the appropriately named properties file in <code>resources.locale</code>.
+ * </ul>
+ * @author C.Miller
+ * @version 1.0
+ */
+public class PackageResourceAdapter extends ResourceAdapter{
+
+ // constructor
+ public PackageResourceAdapter(String propertyFile) throws IOException {
+ super();
+ props = "resources.locale." + propertyFile;
+ init();
+ }
+
+ public URL getHelpURL(String helpURLName) {
+ String path = "/resources/helpfiles/" + bundle.getString("helpURL." + helpURLName);
+ URL url = getClass().getResource(path);
+ return url;
+ }
+
+ public URL getImageURL(String imageName) {
+ String imageFilename = "/resources/images/" + bundle.getString("image." + imageName);
+ URL url = getClass().getResource(imageFilename);
+ return url;
+ }
+}
diff --git a/src/uk/ac/man/bioinf/util/ResourceAdapter.java b/src/uk/ac/man/bioinf/util/ResourceAdapter.java
new file mode 100644
index 0000000..bf468fb
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/ResourceAdapter.java
@@ -0,0 +1,113 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+package uk.ac.man.bioinf.util;
+import java.util.ResourceBundle;
+import java.util.Locale;
+import java.net.URL;
+import java.io.File;
+import java.io.IOException;
+/**
+ * Generic class for locating resources within an application/applet's package
+ * hierarchy. Resources are defined in a locale specific property file according to
+ * the conventions defined in ResourceBundle.
+ * For URLs, looks up the appropriate path in the specified property file,
+ * and then uses that to retrieve a pointer to it.
+ * @author C.Miller
+ * @version 1.0
+ */
+public class ResourceAdapter {
+
+ protected Locale defaultLocale = Locale.getDefault();
+ protected ResourceBundle bundle;
+ protected String props;
+ // constructor
+
+ public ResourceAdapter() {
+ }
+
+ public ResourceAdapter(String propertyFile) throws IOException {
+ props = propertyFile;
+ init();
+ }
+
+
+ protected void init() throws IOException {
+ bundle = ResourceBundle.getBundle(props,defaultLocale);
+ if(bundle == null) throw new IOException("Can't find properties file for resource bundle.");
+ }
+
+ /**
+ * property is message.<messageName>
+ */
+ public String getMessageString(String messageName) {
+ String message = bundle.getString("message." + messageName);
+ return message;
+ }
+
+ /**
+ * property is tooltip.<tooltipName>
+ */
+ public String getToolTip(String tooltipName) {
+ String message = bundle.getString("tooltip." + tooltipName);
+ return message;
+ }
+
+ /**
+ * property is helpURL.<helpURLName>
+ */
+ public URL getHelpURL(String helpURLName) {
+ String message = bundle.getString("helpURL." + helpURLName);
+ URL url = getClass().getResource(message);
+ return url;
+ }
+
+ /**
+ * property is image.<imageName> value should be path to the image
+ */
+ public URL getImageURL(String imageName) {
+ String imageFilename = bundle.getString("image." + imageName);
+ URL url = getClass().getResource(imageFilename);
+ return url;
+ }
+
+ /**
+ * property is file.<fileDescriptor> value should be path to the image
+ */
+ public File getFile(String fileDescriptor) {
+ String fileDesc = bundle.getString("file." + fileDescriptor);
+ File f = new File(fileDesc);
+ return f;
+ }
+
+ /**
+ * property is url.<URLDescriptor> value should be a URL
+ */
+ public URL getURL(String URLDescriptor) {
+ String fileDesc = bundle.getString("url." + URLDescriptor);
+ URL url = getClass().getResource(fileDesc);
+ return url;
+ }
+
+ /**
+ * property is string.<descriptor> value should be a String
+ */
+ public String getTextString(String descriptor) {
+ String fileDesc = bundle.getString("string." + descriptor);
+ return fileDesc;
+ }
+}
+
diff --git a/src/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.java b/src/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.java
new file mode 100644
index 0000000..413348d
--- /dev/null
+++ b/src/uk/ac/man/bioinf/util/SequenceAlignmentToChangeableAdaptor.java
@@ -0,0 +1,93 @@
+/*
+ *This library is free software; you can redistribute it and/or
+ *modify it under the terms of the GNU Lesser General Public
+ *License as published by the Free Software Foundation; either
+ *version 2.1 of the License, or (at your option) any later version.
+ *
+ *This library is distributed in the hope that it will be useful,
+ *but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ *Lesser General Public License for more details.
+ *
+ *You should have received a copy of the GNU Lesser General Public
+ *License along with this library; if not, write to the Free Software
+ *Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+*/
+
+/*
+ * This software was written by Phillip Lord (p.lord at hgmp.mrc.ac.uk)
+ * whilst at the University of Manchester as a Pfizer post-doctoral
+ * Research Fellow.
+ *
+ * The initial code base is copyright by Pfizer, or the University
+ * of Manchester. Modifications to the initial code base are copyright
+ * of their respective authors, or their employers as appropriate.
+ * Authorship of the modifications may be determined from the ChangeLog
+ * placed at the end of this file
+ */
+
+package uk.ac.man.bioinf.util; // Package name inserted by JPack
+import uk.ac.man.bioinf.sequence.alignment.SequenceAlignment;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentEvent;
+import uk.ac.man.bioinf.sequence.alignment.event.AlignmentListener;
+import uk.ac.man.bioinf.sequence.event.SequenceEvent;
+import uk.ac.man.bioinf.sequence.event.SequenceListener;
+
+
+/**
+ * SequenceAlignmentToChangeableAdaptor.java
+ *
+ *
+ * Created: Thu Jul 20 17:57:44 2000
+ *
+ * @author Phillip Lord
+ * @version $Id: SequenceAlignmentToChangeableAdaptor.java,v 1.2 2001/04/11 17:04:43 lord Exp $
+ */
+
+public class SequenceAlignmentToChangeableAdaptor extends ChangeableListenerSupport
+ implements Changeable, SequenceListener, AlignmentListener
+{
+ private SequenceAlignment alignment;
+
+ public SequenceAlignmentToChangeableAdaptor( SequenceAlignment alignment )
+ {
+ this.alignment = alignment;
+ alignment.addAlignmentListener( this );
+ alignment.addSequenceListener( this );
+ }
+
+ public void changeOccurred( SequenceEvent event )
+ {
+ fireChangeEvent( new ChangeableEvent( this ) );
+ }
+
+ public void changeOccurred( AlignmentEvent event )
+ {
+ fireChangeEvent( new ChangeableEvent( this ) );
+ }
+
+ public int hashCode()
+ {
+ return alignment.hashCode();
+ }
+
+ public boolean equals( Object object )
+ {
+ if( !( object instanceof SequenceAlignmentToChangeableAdaptor ) ) return false;
+
+ return alignment.equals( ((SequenceAlignmentToChangeableAdaptor)object).alignment );
+ }
+} // SequenceAlignmentToChangeableAdaptor
+
+
+
+/*
+ * ChangeLog
+ * $Log: SequenceAlignmentToChangeableAdaptor.java,v $
+ * Revision 1.2 2001/04/11 17:04:43 lord
+ * Added License agreements to all code
+ *
+ * Revision 1.1 2000/07/26 13:29:27 lord
+ * Initial checkin
+ *
+ */
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cinema.git
More information about the debian-med-commit
mailing list